| Previous changeset 3:3d86c89f15bf (2019-08-29) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_mannwhitney_de commit c394391dcf541d91ee1dfdc0c3d80cd7a21942ff |
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modified:
MannWhitney_DE.R mannwhitney_de.xml |
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added:
test-data/factor_2col.tsv test-data/factor_3col.tsv test-data/input.csv test-data/input.tsv test-data/result.tsv test-data/result_from_csv.tsv |
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removed:
test-data/filterCells_100.tsv test-data/filtered-0.05.tab test-data/geneMetadata_log.tsv test-data/geneMetadata_nolog.tsv test-data/signature_2columns.tsv test-data/signature_3columns.tsv |
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| diff -r 3d86c89f15bf -r 6916ac5a9ef0 MannWhitney_DE.R --- a/MannWhitney_DE.R Thu Aug 29 05:35:04 2019 -0400 +++ b/MannWhitney_DE.R Thu Nov 30 02:03:53 2023 +0000 |
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| @@ -1,83 +1,88 @@ -#################### -# Differential # -# analysis # -#################### - -# Perform a differential analysis between 2 -# groups of cells. +# Perform a differential analysis between 2 groups of cells. # Example of command # Rscript MannWhitney_DE.R --input <input.tsv> --sep <tab> --colnames <TRUE> --metadata <signature.tsv> --column_name <rate> --fdr <0.01> --output <diff_analysis.tsv> -# load packages that are provided in the conda env -options( show.error.messages=F, - error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(show.error.messages = FALSE, + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, FALSE) + } +) + loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") -warnings() -library(optparse) -#Arguments -option_list = list( +suppressPackageStartupMessages({ + library(optparse) +}) + +sessionInfo() + +option_list <- list( make_option( "--input", default = NA, - type = 'character', + type = "character", help = "Input file that contains log2(CPM +1) values" ), make_option( "--sep", - default = '\t', - type = 'character', + default = "\t", + type = "character", help = "File separator [default : '%default' ]" ), make_option( "--colnames", default = TRUE, - type = 'logical', + type = "logical", help = "Consider first line as header ? [default : '%default' ]" - ), + ), make_option( "--comparison_factor_file", default = NA, - type = 'character', + type = "character", help = " A two column table : cell identifiers and a comparison factor that split cells in two categories (high/low, HOM/HET,...)" ), make_option( "--factor1", - type = 'character', + type = "character", help = "level associated to the control condition in the factor file" - ), + ), make_option( "--factor2", - type = 'character', + type = "character", help = "level associated to the test condition in the factor file" ), make_option( "--fdr", default = 0.01, - type = 'numeric', + type = "numeric", help = "FDR threshold [default : '%default' ]" ), make_option( "--log", - default=FALSE, - action="store_true", - type = 'logical', + default = FALSE, + action = "store_true", + type = "logical", help = "Expression data are log-transformed [default : '%default' ]" ), make_option( "--output", default = "results.tsv", - type = 'character', + type = "character", help = "Output name [default : '%default' ]" ) ) -opt = parse_args(OptionParser(option_list = option_list), - args = commandArgs(trailingOnly = TRUE)) +opt <- parse_args(OptionParser(option_list = option_list), + args = commandArgs(trailingOnly = TRUE)) -if (opt$sep == "tab") {opt$sep = "\t"} -if (opt$sep == "comma") {opt$sep = ","} +if (opt$sep == "tab") { + opt$sep <- "\t" +} +if (opt$sep == "comma") { + opt$sep <- "," +} #Open files data.counts <- read.table( @@ -85,13 +90,13 @@ h = opt$colnames, row.names = 1, sep = opt$sep, - check.names = F + check.names = FALSE ) metadata <- read.table( opt$comparison_factor_file, header = TRUE, - stringsAsFactors = F, + stringsAsFactors = FALSE, sep = "\t", check.names = FALSE, row.names = 1 @@ -100,35 +105,34 @@ metadata <- subset(metadata, rownames(metadata) %in% colnames(data.counts)) # Create two logical named vectors for each factor level of cell signature -factor1_cells <- setNames(metadata[,1] == opt$factor1, rownames(metadata)) -factor2_cells <- setNames(metadata[,1] == opt$factor2, rownames(metadata)) +factor1_cells <- setNames(metadata[, 1] == opt$factor1, rownames(metadata)) +factor2_cells <- setNames(metadata[, 1] == opt$factor2, rownames(metadata)) ## Mann-Whitney test (Two-sample Wilcoxon test) MW_test <- data.frame(t(apply(data.counts, 1, function(x) { do.call("cbind", wilcox.test(x[names(factor1_cells)[factor1_cells]], x[names(factor2_cells)[factor2_cells]]))[, 1:2] -})), stringsAsFactors = F) +})), stringsAsFactors = FALSE) # Benjamini-Hochberg correction and significativity -MW_test$p.adjust <- p.adjust(as.numeric(MW_test$p.value), method = "BH" , n = nrow(MW_test)) -# MW_test$Critical.value <- (rank(MW_test$p.value) / nrow(MW_test)) * opt$fdr +MW_test$p.adjust <- p.adjust(as.numeric(MW_test$p.value), method = "BH", n = nrow(MW_test)) MW_test$Significant <- MW_test$p.adjust < opt$fdr ## Descriptive Statistics Function descriptive_stats <- function(InputData) { - SummaryData = data.frame( + SummaryData <- data.frame( mean = rowMeans(InputData), SD = apply(InputData, 1, sd), Variance = apply(InputData, 1, var), Percentage_Detection = apply(InputData, 1, function(x, y = InputData) { (sum(x != 0) / ncol(y)) * 100 }), - mean_condition2 = rowMeans(InputData[,factor2_cells]), + mean_condition2 = rowMeans(InputData[, factor2_cells]), mean_condition1 = rowMeans(InputData[, factor1_cells]) ) - if(opt$log) { - SummaryData$log2FC <- SummaryData$mean_condition2 - SummaryData$mean_condition1 + if (opt$log) { + SummaryData$log2FC <- SummaryData$mean_condition2 - SummaryData$mean_condition1 } else { - SummaryData$log2FC <- log2(SummaryData$mean_condition2 / SummaryData$mean_condition1) + SummaryData$log2FC <- log2(SummaryData$mean_condition2 / SummaryData$mean_condition1) } return(SummaryData) } @@ -139,16 +143,16 @@ colnames(results)[1] <- "genes" ## Annotate Significant column -results$Significant[results$Significant == T & !is.na(results$Significant)] <- ifelse(subset(results, Significant == T)$log2FC > 0, "UP", "DOWN") -results$Significant[results$Significant == F & !is.na(results$Significant)] <- "NS" +results$Significant[results$Significant == TRUE & !is.na(results$Significant)] <- ifelse(subset(results, Significant == TRUE)$log2FC > 0, "UP", "DOWN") +results$Significant[results$Significant == FALSE & !is.na(results$Significant)] <- "NS" # Save files write.table( - results[order(results$p.adjust),], + results[order(results$p.adjust), ], opt$output, sep = "\t", - quote = F, - col.names = T, - row.names = F + quote = FALSE, + col.names = TRUE, + row.names = FALSE ) |
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| diff -r 3d86c89f15bf -r 6916ac5a9ef0 mannwhitney_de.xml --- a/mannwhitney_de.xml Thu Aug 29 05:35:04 2019 -0400 +++ b/mannwhitney_de.xml Thu Nov 30 02:03:53 2023 +0000 |
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| @@ -1,7 +1,7 @@ -<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.4"> +<tool id="mannwhitney_de" name="Perform a differential analysis" version="4.1.3+galaxy0"> <description>using a Mann-Whitney test</description> <requirements> - <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> + <requirement type="package" version="1.7.1">r-optparse</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -48,37 +48,26 @@ </outputs> <tests> <test> - <param name="input" value="filtered-0.05.tab" ftype="txt"/> - <param name="sep" value="tab" /> - <param name="colnames" value="TRUE"/> - <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/> - <param name="factor1" value="LOW"/> - <param name="factor2" value="HIGH"/> - <param name="fdr" value="0.01"/> - <param name="log" value="true"/> - <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/> - </test> - <test> - <param name="input" value="filtered-0.05.tab" ftype="txt"/> + <param name="input" value="input.tsv" ftype="tabular"/> <param name="sep" value="tab" /> <param name="colnames" value="TRUE"/> - <param name="comparison_factor_file" value="signature_3columns.tsv" ftype="tabular"/> + <param name="comparison_factor_file" value="factor_2col.tsv" ftype="tabular"/> <param name="factor1" value="LOW"/> <param name="factor2" value="HIGH"/> - <param name="fdr" value="0.01"/> + <param name="fdr" value="0.05"/> <param name="log" value="true"/> - <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/> + <output name="output" file="result.tsv" ftype="tabular"/> </test> <test> - <param name="input" value="filterCells_100.tsv" ftype="txt"/> - <param name="sep" value="tab" /> + <param name="input" value="input.csv" ftype="txt"/> + <param name="sep" value="comma" /> <param name="colnames" value="TRUE"/> - <param name="comparison_factor_file" value="signature_2columns.tsv" ftype="tabular"/> + <param name="comparison_factor_file" value="factor_3col.tsv" ftype="tabular"/> <param name="factor1" value="LOW"/> <param name="factor2" value="HIGH"/> - <param name="fdr" value="0.01"/> - <param name="log" value="false"/> - <output name="output" file="geneMetadata_nolog.tsv" ftype="tabular"/> + <param name="fdr" value="0.05"/> + <param name="log" value="true"/> + <output name="output" file="result_from_csv.tsv" ftype="tabular"/> </test> </tests> <help> |
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| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/factor_2col.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/factor_2col.tsv Thu Nov 30 02:03:53 2023 +0000 |
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| @@ -0,0 +1,101 @@ +cell rate +c173.B4 LOW +c173.A2 LOW +c173.E2 LOW +c173.F6 LOW +c173.B12 LOW +c173.H1 HIGH +c173.E4 HIGH +c173.C2 LOW +c173.F4 LOW +c173.E10 HIGH +c173.E6 LOW +c173.C4 HIGH +c173.B10 LOW +c173.A7 LOW +c173.B8 LOW +c173.F9 LOW +c173.G6 HIGH +c173.A9 LOW +c173.D2 HIGH +c173.F2 LOW +c173.H9 LOW +c173.G1 LOW +c173.B3 LOW +c173.D7 HIGH +c173.A12 LOW +c173.C1 LOW +c173.H7 HIGH +c173.H5 LOW +c173.G2 LOW +c173.A3 LOW +c173.D3 LOW +c173.E1 LOW +c173.G12 HIGH +c173.C10 HIGH +c173.C3 LOW +c173.A5 LOW +c173.G4 LOW +c173.B11 LOW +c173.G9 HIGH +c173.F1 LOW +c173.D8 LOW +c173.E12 HIGH +c173.F11 LOW +c173.E5 LOW +c173.G10 LOW +c173.B9 LOW +c173.C7 HIGH +c173.B2 LOW +c173.H4 LOW +c174.G5 LOW +c174.H9 LOW +c174.A10 LOW +c174.G10 HIGH +c174.C8 LOW +c174.F6 LOW +c174.B4 LOW +c174.H7 LOW +c174.E10 HIGH +c174.D5 LOW +c174.E5 LOW +c174.B11 LOW +c174.F10 LOW +c174.A5 LOW +c174.B8 LOW +c174.F2 LOW +c174.F9 HIGH +c174.F4 HIGH +c174.B6 LOW +c174.E2 LOW +c174.G2 LOW +c174.D8 LOW +c174.H6 LOW +c174.C3 HIGH +c174.B7 LOW +c174.A7 LOW +c174.H10 LOW +c174.F7 HIGH +c174.A2 LOW +c174.E4 LOW +c174.D12 LOW +c174.H4 LOW +c174.C5 LOW +c174.E9 LOW +c174.D1 LOW +c174.G4 LOW +c174.G9 LOW +c174.D4 HIGH +c174.H11 HIGH +c174.A9 LOW +c174.A4 HIGH +c174.C7 LOW +c174.D11 LOW +c174.F5 LOW +c174.G6 LOW +c174.D6 LOW +c174.H3 LOW +c174.F12 LOW +c174.E6 LOW +c174.G3 LOW +c174.A8 LOW |
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| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/factor_3col.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/factor_3col.tsv Thu Nov 30 02:03:53 2023 +0000 |
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| @@ -0,0 +1,101 @@ +cell rate extra +c173.B4 LOW 2 +c173.A2 LOW 3 +c173.E2 LOW 4 +c173.F6 LOW 5 +c173.B12 LOW 6 +c173.H1 HIGH 7 +c173.E4 HIGH 8 +c173.C2 LOW 9 +c173.F4 LOW 10 +c173.E10 HIGH 11 +c173.E6 LOW 12 +c173.C4 HIGH 13 +c173.B10 LOW 14 +c173.A7 LOW 15 +c173.B8 LOW 16 +c173.F9 LOW 17 +c173.G6 HIGH 18 +c173.A9 LOW 19 +c173.D2 HIGH 20 +c173.F2 LOW 21 +c173.H9 LOW 22 +c173.G1 LOW 23 +c173.B3 LOW 24 +c173.D7 HIGH 25 +c173.A12 LOW 26 +c173.C1 LOW 27 +c173.H7 HIGH 28 +c173.H5 LOW 29 +c173.G2 LOW 30 +c173.A3 LOW 31 +c173.D3 LOW 32 +c173.E1 LOW 33 +c173.G12 HIGH 34 +c173.C10 HIGH 35 +c173.C3 LOW 36 +c173.A5 LOW 37 +c173.G4 LOW 38 +c173.B11 LOW 39 +c173.G9 HIGH 40 +c173.F1 LOW 41 +c173.D8 LOW 42 +c173.E12 HIGH 43 +c173.F11 LOW 44 +c173.E5 LOW 45 +c173.G10 LOW 46 +c173.B9 LOW 47 +c173.C7 HIGH 48 +c173.B2 LOW 49 +c173.H4 LOW 50 +c174.G5 LOW 51 +c174.H9 LOW 52 +c174.A10 LOW 53 +c174.G10 HIGH 54 +c174.C8 LOW 55 +c174.F6 LOW 56 +c174.B4 LOW 57 +c174.H7 LOW 58 +c174.E10 HIGH 59 +c174.D5 LOW 60 +c174.E5 LOW 61 +c174.B11 LOW 62 +c174.F10 LOW 63 +c174.A5 LOW 64 +c174.B8 LOW 65 +c174.F2 LOW 66 +c174.F9 HIGH 67 +c174.F4 HIGH 68 +c174.B6 LOW 69 +c174.E2 LOW 70 +c174.G2 LOW 71 +c174.D8 LOW 72 +c174.H6 LOW 73 +c174.C3 HIGH 74 +c174.B7 LOW 75 +c174.A7 LOW 76 +c174.H10 LOW 77 +c174.F7 HIGH 78 +c174.A2 LOW 79 +c174.E4 LOW 80 +c174.D12 LOW 81 +c174.H4 LOW 82 +c174.C5 LOW 83 +c174.E9 LOW 84 +c174.D1 LOW 85 +c174.G4 LOW 86 +c174.G9 LOW 87 +c174.D4 HIGH 88 +c174.H11 HIGH 89 +c174.A9 LOW 90 +c174.A4 HIGH 91 +c174.C7 LOW 92 +c174.D11 LOW 93 +c174.F5 LOW 94 +c174.G6 LOW 95 +c174.D6 LOW 96 +c174.H3 LOW 97 +c174.F12 LOW 98 +c174.E6 LOW 99 +c174.G3 LOW 100 +c174.A8 LOW 101 |
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| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/filterCells_100.tsv --- a/test-data/filterCells_100.tsv Thu Aug 29 05:35:04 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,23369 +0,0 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|
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/filtered-0.05.tab --- a/test-data/filtered-0.05.tab Thu Aug 29 05:35:04 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,43 +0,0 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13225221491\t0\t0\t0\t0\t0\t0\t0\t0\t16.8049477311572\t0\t0\t0\t0\t0\t0\t0\t13.1609986763417\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8.83636708837122\t0\t0\t0\t17.463590172088\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t9.1875306716268\t0\t0\t13.5241872063119\t18.0750354938906\t0\t0\t10.2810788111136\t17.2459745865081\t15.9279160530013\t12.748556401713\t0\t0\t0\t0\t0\n-DUSP14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t17.682339347864\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t15.315185545429\t13.7402034707105\t0\t0\t0\t0\t0\t0\t0\t0\t0\t13.0068022983915\t16.2881643662067\t0\t0\t9.93304513317431\t0\t0\t0\t0\t0\t0\t16.1889386483903\t0\t0\t0\t0\t0\t0\t0\t0\t14.2903113142977\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8.92960758696251\t0\t0\t0\t0\t0\t9.58251231821503\t0\t0\t0\t0\t0\t0\t0\n-LSAMP\t0\t0\t0\t14.6759892692826\t0\t0\t0\t12.0533461710639\t0\t17.443105373872\t0\t0\t0\t0\t18.0085029188716\t14.9703906666539\t0\t0\t0\t0\t15.1097945143932\t16.4778545804206\t0\t10.3189090138321\t0\t0\t16.8967216358908\t10.0381235983496\t0\t0\t16.5804778250305\t0\t14.0965479473356\t15.1259052017533\t0\t0\t14.4671092099988\t0\t15.3127843769133\t0\t7.58238867217773\t17.0198239388304\t0\t0\t0\t8.04450047834992\t0\t0\t0\t0\t0\t13.968540182416\t15.71562514092\t15.2670695731409\t0\t0\t16.0848565947262\t16.8549278933251\t0\t0\t15.0084279381472\t0\t0\t0\t0\t9.64220443531159\t12.2810179092402\t17.0312914793051\t12.2426279199397\t14.4957467346967\t17.5289904393214\t0\t0\t0\t0\t17.4281796010913\t7.97406042331398\t0\t0\t0\t17.2062943205767\t9.24744364660748\t0\t0\t9.1875306716268\t0\t0\t0\t0\t0\t17.2240719991621\t18.2874179157258\t0\t0\t0\t0\t0\t13.639885471395\t0\t0\n-IFRD2\t0\t14.1567591557826\t0\t0\t14.957471072991\t0\t11.7467317882544\t12.6777177703235\t0\t0\t0\t14.9692054355984\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t16.1887921858769\t0\t0\t0\t0\t0\t0\t0\t13.3325488559645\t0\t0\t15.4049392399236\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11.9828942206529\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t15.220111460789\t0\t0\t0\t0\t0\t15.9054397866496\n-PSMC3\t0\t13.2005548043296\t14.8560845850134\t13.9643699083462\t0\t0\t15.3496874953813\t10.7907868950769\t0\t15.1318370018154\t0\t9.04707783388214\t0\t8.19629321739164\t8.79017289622793\t0\t0\t15.8347317159755\t0\t0\t0\t17.0608232736151\t0\t0\t0\t13.5804315841045\t0\t16.8246657947268\t0\t0\t0\t0\t14.0034440332771\t13.6639750287706\t9.87731250666145\t15.9198563257041\t14.9976043265065\t8.23765146833625\t14.0590768628974\t0\t0\t9.47110050463318\t0\t0\t0\t15.9579116555843\t14.8885374422562\t0\t0\t9.20185308314151\t17.7774040608022\t15.4550410979026\t0\t0\t0\t12.7812138562999\t13.3160965297846\t13.362283927802\t0\t16.4148573168466\t0\t16.3937707725726\t0\t0\t16.275541157128\t7.77254179434776\t16.4506691081895\t0\t17.0179871238337\t0\t0\t12.4571973732293\t0\t18.4730583687277\t0\t0\t0\t14.7148366132387\t0\t14.1156444482226\t0\t0\t0\t0\t0\t0\t14.2842702042516\t0\t0\t16.3258394378728\t16.0093455986421\t0\t0\t12.9572206787611\t0\t0\t0\t13.4841036871113\t0\t9.22834347315191\n-MUM1\t0\t0\t0\t12.6633325294353\t0\t0\t0\t14.5555669503357\t0\t13.3179500884142\t0\t0\t0\t0\t16.5748276652721\t0\t0\t0\t0\t0\t13.6318200750724\t0\t0\t12.710311816626\t0\t0\t18.214454853308\t15.1660730637326\t0\t0\t0\t0\t14.7518697094683\t7.00273235200855\t0\t0\t14.1650955067633\t0\t0\t0\t0\t0\t0\t13.2917085826559\t0\t0\t12.2258260817879\t0\t0\t0\t0\t0\t0\t11.886990211753\t11.7235170132018\t0\t0\t0\t0\t0\t0\t0\t18.3760540871383\t0\t0\t0\t12.6529208030743\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11.244072167057\t0\t0\t0\t0\t14.4820702391067\t14.2768099711357\t0\t16.0313326070449\t16.1554843460377\t0\t0\t15.7728280344041\t10.6703592668752\t0\t0\t13.6708456975204\t0\t0\t0\t13.8991097089352\t0\t0\n-DIAPH2\t0\t0\t0\t0\t14.2205357083466\t16.7152640709125\t0\t0\t0\t0\t0\t0\t0\t16.654904535232\t0\t0\t0\t9.08248316789768\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t15.4373454971523\t0\t0\t0\t0\t0\t0\t0\t15.0941747307558\t0\t0\t0\t0\t0\t13.8406723774638\t0\t11.5418835561333\t0\t0\t0\t0\t15.3892593189199\t0\t0\t0\t0\t0\t11.3076469757304\t0\t0\t0\t13.3508485655876\t0\t0\t14.3317256961498\t0\t0\t0\t0\t0\t0\t0\t0\t10.8056703376854\t0\t0\t0\t0\t0\t10.9546977217628\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t11.7742726683055\t0\t0\t0\t0\t13.9279854762358\t8.84459780169115\t0\t10.3514726687616\t0\t0\t11.548346056541\n' |
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/geneMetadata_log.tsv --- a/test-data/geneMetadata_log.tsv Thu Aug 29 05:35:04 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,43 +0,0 @@ -genes mean SD Variance Percentage_Detection mean_condition2 mean_condition1 log2FC statistic p.value p.adjust Significant -ACAD9 3.21757044598762 6.03354965169885 36.4037213995154 23 2.88532585223158 3.38872675186193 -0.50340089963035 6 0.411313791776259 1 NS -APIP 1.48573169701519 4.42462910898839 19.5773427521074 11 1.36959754030536 1.5455583838051 -0.175960843499742 5 0.723673609831763 1 NS -BAI3 1.40915813751371 4.12336508696455 17.0021396403981 11 1.41059944781951 1.40841564432588 0.00218380349363256 5 0.723673609831763 1 NS -C3orf62 2.21928690308303 5.23726221704512 27.4289155300884 16 1.99337186851464 2.33566737543644 -0.342295506921804 2 0.288844366346485 1 NS -CCT4 5.58991399452656 7.04582138621306 49.6435990064173 40 5.97697998966529 5.39051636066721 0.586463628998078 5.5 0.63859207768502 1 NS -CDKN2A 3.14847608508595 5.97643617835182 35.7177893939125 22 2.85206036997725 3.30117508983891 -0.449114719861661 5 0.8 1 NS -CHTOP 4.95213087424945 6.69826385145611 44.8667386237237 37 5.12715074739128 4.86196912141881 0.265181625972471 4.5 1 1 NS -CLPB 1.20688850619883 3.94292278228986 15.5466400671004 9 1.64019045303295 0.983672351769125 0.656518101263825 3.5 1 1 NS -COQ7 1.81109934358668 4.59246883791874 21.0907700272547 14 2.81750977159578 1.2926454867335 1.52486428486228 3 0.805732790848439 1 NS -DIAPH2 2.45173786931265 5.19109016758801 26.9474171280289 19 1.90478386205171 2.73350205487132 -0.828718192819611 2 0.288844366346485 1 NS -FAM63B 2.44551578150534 5.13806432586195 26.3997050166952 20 1.25193652944719 3.0603899416565 -1.80845341220932 3.5 1 1 NS -GAPDH 17.6727587681588 4.98787838098139 24.8789307434615 93 18.3959280065131 17.3002170393096 1.09571096720344 0 0.133333333333333 1 NS -H3F3C 2.69750936927498 4.35063868472497 18.9280569650254 29 2.19689835219708 2.95539989322421 -0.758501541027127 6 0.411313791776259 1 NS -IFRD2 1.56542610972806 4.50279575682847 20.2751696277125 11 1.73709044769323 1.47699296592783 0.260097481765406 1 0.218819415823491 1 NS -ITGB1 5.73749610754924 6.96917363119079 48.569381101685 42 5.92731202994722 5.63971214752604 0.287599882421176 2 0.288844366346485 1 NS -LSAMP 5.40538485683009 7.20340373028298 51.8890253014547 38 7.456451258236 4.34877489246947 3.10767636576653 8 0.133333333333333 1 NS -MUM1 3.59113963428165 6.20728875372071 38.5304336720676 26 3.26567136238311 3.75880510768392 -0.493133745300816 5.5 0.63859207768502 1 NS -NCAPH2 2.09924645828476 4.9160781393554 24.167824272248 16 2.7402301291671 1.76904274904235 0.971187380124752 5 0.723673609831763 1 NS -OBFC2B 2.56257992189769 5.37946105314442 28.9386012222977 19 2.50827678586446 2.59055426470269 -0.0822774788382348 3.5 1 1 NS -PSMC3 6.17973106872374 7.13113762893614 50.8531238828289 45 6.07099348144692 6.23574740156331 -0.164753920116381 2 0.460633522588757 1 NS -PSPH 3.45898367616203 5.82691731716674 33.9529654210976 27 3.23100704116237 3.57642618510125 -0.345419143938882 8 0.133333333333333 1 NS -RABL5 3.2703554589894 5.97444372569743 35.6939778315254 24 3.69997306551525 3.04903729805185 0.650935767463402 4 1 1 NS -RNF185 1.46932887276529 4.13672007089318 17.1124529449304 12 1.06620456119726 1.67699897266398 -0.610794411466722 2 0.288844366346485 1 NS -SIN3A 4.00526302988229 6.32973969419456 40.0656045962622 30 4.28049583047595 3.86347643563706 0.417019394838893 2.5 0.583882420770365 1 NS -SLC15A4 2.6490939213568 5.36541152568955 28.7876408400022 21 2.38443898616311 2.78543131221415 -0.400992326051037 5 0.723673609831763 1 NS -SMYD3 1.11766527425951 3.45565630150241 11.9415604741133 10 1.17955973857534 1.08578024718772 0.0937794913876244 6 0.411313791776259 1 NS -TBC1D15 2.64803303609142 5.30241142820209 28.1155669539282 21 4.13093321985626 1.88411475960651 2.24681846024975 4 1 1 NS -ZFHX4 2.71178769759176 5.4146903421813 29.3188715017114 21 2.51282638206758 2.81428292074058 -0.301456538672999 4 1 1 NS -ZNF454 0.922860300134436 3.46176149331655 11.9837926366092 7 2.03306973832583 0.350934225914629 1.6821355124112 5 0.723673609831763 1 NS -ZNF780B 1.00358719015216 3.48539676962484 12.1479906417113 8 1.5525594677108 0.720783289591644 0.831776178119159 5 0.723673609831763 1 NS -AKT1 3.4403135511678 6.3127111628083 39.8503222250445 24 3.29486356822599 3.51524233025904 -0.220378762033048 4 NaN NA NA -BPHL 1.8725575575664 4.76402741808616 22.6959572402767 14 2.36794096575365 1.61736004425781 0.750580921495835 4 NaN NA NA -CHFR 3.2793294035845 6.00856983357212 36.1029114449129 24 2.69677094764966 3.57943527482366 -0.882664327174004 4 NaN NA NA -CNOT10 1.35116986328472 4.15039762997951 17.2258004869395 10 0.769393328753782 1.65087292652794 -0.881479597774154 4 NaN NA NA -CYTH4 3.15940473609362 6.446078714101 41.5519307883859 20 2.52965691299695 3.48382028132524 -0.954163368328291 4 NaN NA NA -DUSP14 1.34957110029642 4.17409370205428 17.4230582335292 10 1.22165867778853 1.41546537855805 -0.193806700769524 4 NaN NA NA -ISOC2 1.35653919273248 4.13500630208934 17.0982771183186 10 1.16088000029635 1.45733332216928 -0.296453321872929 4 NaN NA NA -LAIR1 5.14073096940228 7.67228689265092 58.8639861631431 32 3.00047442611951 6.24328737048734 -3.24281294436782 4 NaN NA NA -MYO7A 2.08943827729343 5.13674406841985 26.3861396244465 15 2.09929129953666 2.084362477956 0.0149288215806527 4 NaN NA NA -PARVB 2.21851609168455 4.93366814223579 24.3410813377123 18 2.08303594275959 2.28830889567619 -0.205272952916603 4 NaN NA NA -SLC4A5 1.85823253159878 4.89934798569655 24.0036106849488 13 2.14955177017941 1.70815898445118 0.441392785728234 4 NaN NA NA -TMEM132C 0.822592049405892 3.30504805041197 10.923342615532 6 2.0849055246802 0.172309350022156 1.91259617465805 4 NaN NA NA |
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/geneMetadata_nolog.tsv --- a/test-data/geneMetadata_nolog.tsv Thu Aug 29 05:35:04 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,23369 +0,0 @@\n-genes\tmean\tSD\tVariance\tPercentage_Detection\tmean_condition2\tmean_condition1\tlog2FC\tstatistic\tp.value\tp.adjust\tSignificant\n-CHTOP\t60.47\t118.911600728772\t14139.9687878788\t55\t163.318181818182\t31.4615384615385\t2.37602428656421\t175\t2.57033171062643e-09\t6.00635114139184e-05\tUP\n-GALNS\t35.44\t78.0910269163397\t6098.20848484848\t32\t113.818181818182\t13.3333333333333\t3.09362163412911\t303.5\t2.58580026024812e-08\t0.000158156330665433\tUP\n-PPP1CA\t115.66\t136.955070417752\t18756.6913131313\t68\t274.954545454545\t70.7307692307692\t1.95878328044117\t197\t2.29268329304412e-08\t0.000158156330665433\tUP\n-STT3A\t83.61\t112.034166415627\t12551.6544444444\t73\t206.545454545455\t48.9358974358974\t2.07749424851407\t196\t2.70722921371847e-08\t0.000158156330665433\tUP\n-CALR\t159.63\t202.286458301393\t40919.8112121212\t82\t389.454545454545\t94.8076923076923\t2.03837893298878\t207.5\t5.80141758382607e-08\t0.000225945876831413\tUP\n-CLIC4\t327.59\t384.665251165927\t147967.355454545\t89\t725.454545454545\t215.371794871795\t1.75205589604189\t202.5\t4.92765558547744e-08\t0.000225945876831413\tUP\n-HLA-A\t473.68\t534.845977640273\t286060.21979798\t90\t1110.63636363636\t294.025641025641\t1.91737265904105\t209.5\t6.86227724892689e-08\t0.000226705983157064\tUP\n-QSOX1\t16.98\t45.629597872655\t2082.0602020202\t23\t59.7727272727273\t4.91025641025641\t3.60561710247966\t381.5\t7.76124557196385e-08\t0.000226705983157064\tUP\n-ACAD9\t58.95\t108.585336268417\t11790.7752525253\t50\t140.909090909091\t35.8333333333333\t1.975390532656\t264\t1.29568560680755e-07\t0.000288927726822268\tUP\n-CD59\t229.24\t320.388877346378\t102649.032727273\t76\t550.545454545455\t138.615384615385\t1.98977429367599\t228.5\t1.3600671837748e-07\t0.000288927726822268\tUP\n-PDIA3\t140.98\t172.160659052097\t29639.2925252525\t78\t333.909090909091\t86.5641025641026\t1.94761459224942\t226.5\t1.29965189511026e-07\t0.000288927726822268\tUP\n-P4HB\t236.06\t325.508609639584\t105955.854949495\t75\t592.227272727273\t135.602564102564\t2.12676647117757\t235\t1.78273807482546e-07\t0.000347158527771011\tUP\n-APLP2\t225.47\t262.262435261886\t68781.584949495\t80\t475.318181818182\t155\t1.61662537300636\t247\t3.38841618327491e-07\t0.000404577578641395\tUP\n-BOD1\t42.64\t72.2448865758929\t5219.32363636364\t43\t111.772727272727\t23.1410256410256\t2.2720434980465\t303\t3.19745392726432e-07\t0.000404577578641395\tUP\n-CDKN2A\t292.13\t424.457220959006\t180163.932424242\t92\t733.181818181818\t167.730769230769\t2.12802364246519\t243.5\t3.21435910950314e-07\t0.000404577578641395\tUP\n-CFL1\t610.28\t532.430620130478\t283482.365252525\t95\t1147.81818181818\t458.666666666667\t1.32337616314475\t244\t3.30381731831549e-07\t0.000404577578641395\tUP\n-CHUK\t9.77\t38.721188050477\t1499.3304040404\t13\t35.8636363636364\t2.41025641025641\t3.89526323856077\t499\t3.31663050726648e-07\t0.000404577578641395\tUP\n-CPNE4\t6.83\t31.7261180363524\t1006.54656565657\t9\t31\t0.0128205128205128\t11.2395985292491\t553.5\t3.47743032646583e-07\t0.000404577578641395\tUP\n-DRAP1\t41.71\t52.5265291317279\t2759.03626262626\t78\t92.4545454545455\t27.3974358974359\t1.75470337142264\t248\t3.41235083703636e-07\t0.000404577578641395\tUP\n-ENO1\t791.6\t886.202886226148\t785355.555555556\t89\t1683.81818181818\t539.948717948718\t1.64084206723023\t243\t3.1109486520715e-07\t0.000404577578641395\tUP\n-LPHN2\t4.84\t17.7688411882069\t315.731717171717\t9\t20.7272727272727\t0.358974358974359\t5.85150569233209\t554\t3.63579645304232e-07\t0.000404577578641395\tUP\n-GUK1\t303.35\t334.56772577658\t111935.563131313\t86\t674.272727272727\t198.730769230769\t1.76251698475578\t251.5\t4.43117570448923e-07\t0.000450207451576106\tUP\n-TMED2\t105.52\t144.516433653615\t20884.9995959596\t58\t226.590909090909\t71.3717948717949\t1.66666402164468\t273.5\t4.41739919749107e-07\t0.000450207451576106\tUP\n-CDC23\t17.35\t46.9761114877025\t2206.75505050505\t23\t42.1363636363636\t10.3589743589744\t2.02418464609869\t411\t4.66574408336576e-07\t0.000454287948917046\tUP\n-GNAS\t273.8\t245.316987268359\t60180.4242424242\t92\t514.909090909091\t205.794871794872\t1.32311070952795\t253.5\t4.97712059193236e-07\t0.000465221415969102\tUP\n-MRPS15\t58.56\t107.04896642248\t11459.4812121212\t48\t151.409090909091\t32.3717948717949\t2.22564256637278\t299.5\t5.485536393'..b'\tNA\tNA\n-WFDC13\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WFDC5\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WFDC6\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WFDC8\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WFDC9\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WFIKKN2\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WISP2\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WISP3\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNK2\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNT10B\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNT11\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNT2\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNT6\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNT7B\t0\t0\t0\t0\t0\t0\tNA\t858\tNaN\tNA\tNA\n-WNT8A\t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|
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/input.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.csv Thu Nov 30 02:03:53 2023 +0000 |
| b |
| b'@@ -0,0 +1,1001 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|
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/input.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.tsv Thu Nov 30 02:03:53 2023 +0000 |
| b |
| b'@@ -0,0 +1,1001 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|
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/result.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.tsv Thu Nov 30 02:03:53 2023 +0000 |
| b |
| b'@@ -0,0 +1,1001 @@\n+genes\tmean\tSD\tVariance\tPercentage_Detection\tmean_condition2\tmean_condition1\tlog2FC\tstatistic\tp.value\tp.adjust\tSignificant\n+CHTOP\t3.8234613519\t3.84537289419585\t14.7868926954161\t55\t7.93857243409091\t2.66278899538462\t5.27578343870629\t221\t2.77104282187417e-08\t1.38552141093708e-05\tUP\n+GALNS\t2.2481162207\t3.51579961231222\t12.3608469139348\t32\t6.08584531863636\t1.16567980846154\t4.92016551017482\t298.5\t1.93694184665631e-08\t1.38552141093708e-05\tUP\n+ACAD9\t3.6175666278\t3.92373892857361\t15.395727179604\t50\t7.65313508727273\t2.47932937\t5.17380571727273\t252.5\t7.38169087242701e-08\t1.70542874108158e-05\tUP\n+PPP1CA\t5.5439969757\t4.24633823493944\t18.0313884055086\t68\t9.56443781545454\t4.4100264824359\t5.15441133301865\t216\t5.71634864068665e-08\t1.70542874108158e-05\tUP\n+QSOX1\t1.4023561952\t2.80910384050578\t7.89106438674434\t23\t4.37727818863636\t0.563275632948718\t3.81400255568765\t383\t8.52714370540792e-08\t1.70542874108158e-05\tUP\n+CALR\t6.1332206259\t3.74330853958279\t14.0123588225134\t82\t9.46178946409091\t5.19439351769231\t4.2673959463986\t228\t1.49386785685187e-07\t2.13409693835981e-05\tUP\n+STT3A\t5.236738824\t3.62605148242273\t13.1482493531801\t73\t8.46855458454545\t4.32520104538462\t4.14335353916084\t230\t1.33870514441858e-07\t2.13409693835981e-05\tUP\n+CHUK\t0.8719910028\t2.46162223204938\t6.05958401331976\t13\t3.16185595909091\t0.226131656153846\t2.93572430293706\t497\t2.85188510211347e-07\t3.56485637764184e-05\tUP\n+CPNE4\t0.526141333\t1.86358339179453\t3.47294305817242\t9\t2.32411542863636\t0.0190204342307692\t2.30509499440559\t553\t3.32791497459475e-07\t3.69768330510528e-05\tUP\n+CDKN2A\t7.6964229078\t3.10484757262992\t9.6400784492659\t92\t10.2291212545455\t6.98207209205128\t3.24704916249417\t248\t3.91842117256886e-07\t3.91842117256886e-05\tUP\n+LPHN2\t0.651253002\t2.13715406340722\t4.56742749073799\t9\t2.65581755227273\t0.0858630006410256\t2.5699545516317\t557\t4.73339607180964e-07\t4.30308733800876e-05\tUP\n+BOD1\t3.1497567495\t3.83739924686455\t14.7256329798366\t43\t6.73838572045454\t2.1375793474359\t4.60080637301865\t320\t7.2464212338475e-07\t5.17325024039576e-05\tUP\n+L3MBTL4\t0.9526289915\t2.43611634678434\t5.93466285506989\t16\t3.04302798727273\t0.36302927474359\t2.67999871252914\t478.5\t7.75987536059364e-07\t5.17325024039576e-05\tUP\n+RAB11FIP2\t1.1953109236\t2.4244277791648\t5.87785005638597\t22\t3.54252472954545\t0.533276260384615\t3.00924846916084\t424.5\t6.68529681059636e-07\t5.17325024039576e-05\tUP\n+TMED2\t4.8793516487\t4.43931839493608\t19.7075478116179\t58\t8.71889055227273\t3.79640477846154\t4.92248577381119\t286\t7.73621573695859e-07\t5.17325024039576e-05\tUP\n+CDC23\t1.4845877429\t2.93586935370758\t8.61932886203936\t23\t4.03794072045455\t0.764411262051282\t3.27352945840326\t422\t8.85938244801212e-07\t5.42768494562811e-05\tUP\n+KPNA6\t4.2484375509\t3.96585005887565\t15.727966689484\t60\t7.92728396\t3.21081420474359\t4.71646975525641\t288\t9.68141352346355e-07\t5.42768494562811e-05\tUP\n+MRPS15\t3.4301327823\t3.80590294950846\t14.4848972610772\t48\t6.82621584818182\t2.47226319961538\t4.35395264856643\t312\t9.76983290213059e-07\t5.42768494562811e-05\tUP\n+P4HB\t6.4598457483\t4.16631767129325\t17.3582029381304\t75\t9.84999056590909\t5.50365105615385\t4.34633950975524\t279\t1.22440375342796e-06\t6.1220187671398e-05\tUP\n+PDIA3\t5.8247363125\t3.87278033056344\t14.9984274887991\t78\t9.02030213909091\t4.92342287423077\t4.09687926486014\t277\t1.19671614202614e-06\t6.1220187671398e-05\tUP\n+GUK1\t7.5341423268\t3.66254878000738\t13.4142635659336\t86\t10.2908856654545\t6.75659933384615\t3.53428633160839\t281\t1.55859949560046e-06\t7.08454316182027e-05\tUP\n+NIPSNAP1\t1.5822353837\t3.00392732829468\t9.02357939367564\t25\t4.27341426090909\t0.823184931153846\t3.45022932975524\t418.5\t1.55424820873594e-06\t7.08454316182027e-05\tUP\n+ATL3\t1.684943722\t3.06419654740369\t9.38930048112069\t28\t4.27152092409091\t0.955396306025641\t3.31612461806527\t406.5\t2.13583627347771e-06\t7.35991999095773e-05\tUP\n+AXL\t1.8516205135\t2.99984696420088\t8.99908180862526\t33\t4.53106485\t1.09587980320513\t3.43518504679487\t380\t2.02019519292425e-06\t7.35991999095773e-05\tUP\n+C20orf27\t2.2550394962\t3.30651005019324\t10.9330087120289\t35\t5.24810855863636\t1.41084052987179\t3.83'..b'3197307692\t2.15180041132867\t610\t0.000915771581669754\t0.000938290554989502\tUP\n+VTI1A\t0.918271115\t2.40141254119344\t5.76678219300114\t15\t2.60313627136364\t0.443052737564103\t2.16008353379953\t610\t0.000915771581669754\t0.000938290554989502\tUP\n+NUP62\t2.9233171576\t3.70711604126724\t13.7427093434209\t43\t5.35756743454545\t2.23673374615385\t3.12083368839161\t498\t0.000920215840387792\t0.000941879058738784\tUP\n+DIABLO\t3.7530156708\t4.11035117966103\t16.8949868201408\t50\t6.38383409136364\t3.0109899624359\t3.37284412892774\t485\t0.000921429874995332\t0.000942157336396045\tUP\n+DOCK1\t1.0103905969\t2.34412722793681\t5.49493246075471\t19\t2.82872530454545\t0.497526961410256\t2.3311983431352\t585\t0.000924992572007006\t0.00094386997143572\tUP\n+WDR41\t2.5437584238\t3.45241040356169\t11.919137594621\t40\t4.47408604136364\t1.99930704448718\t2.47477899687646\t505\t0.000924513499482298\t0.00094386997143572\tUP\n+FIBP\t4.8655737859\t3.99732726063749\t15.9786252286356\t64\t7.44026504590909\t4.1393788151282\t3.30088623078089\t469\t0.000930327619459469\t0.000946416703417568\tUP\n+PRDX2\t5.7032473587\t4.17744859763615\t17.4510767858922\t70\t8.01002814454545\t5.05261688064103\t2.95741126390443\t465\t0.000929870174709466\t0.000946416703417568\tUP\n+SHC1\t5.8777250291\t3.80971249390208\t14.5139092861936\t77\t8.27128381863636\t5.20261870384615\t3.06866511479021\t462\t0.000929326998154864\t0.000946416703417568\tUP\n+FRS3\t0.4746996647\t1.53251529999738\t2.34860314472606\t9\t1.39806345772727\t0.214263723076923\t1.18379973465035\t660\t0.000931672286839587\t0.000946821429715027\tUP\n+COPZ1\t4.8018366619\t4.07769758494424\t16.6276175942601\t62\t7.37968796181818\t4.07475039782051\t3.30493756399767\t471\t0.000939584042631959\t0.000951959516344437\tUP\n+MRPL24\t3.0131018049\t3.6185920836997\t13.0942086682141\t44\t5.21605900772727\t2.39175490153846\t2.82430410618881\t496.5\t0.000938674990049157\t0.000951959516344437\tUP\n+PSAP\t8.5924321321\t3.44981991233812\t11.9012574275646\t92\t10.5277436009091\t8.04657505115385\t2.48116854975524\t460\t0.000938309531697593\t0.000951959516344437\tUP\n+APPL1\t2.5947342267\t3.45335825941766\t11.9256832678882\t39\t4.67491950090909\t2.00801530320513\t2.66690419770396\t508\t0.000941000129450867\t0.000952301553157109\tUP\n+POM121\t4.9834764401\t3.10875721757676\t9.66437143783559\t83\t6.75950544954545\t4.48254518102564\t2.27696026851981\t461\t0.000941826236072381\t0.000952301553157109\tUP\n+TAF10\t4.8993251071\t3.53777356074795\t12.5158417671272\t71\t7.01148492636364\t4.30358772217949\t2.70789720418415\t465\t0.000944740437866639\t0.000954283270572363\tUP\n+THBS3\t3.1992032815\t3.42246479100473\t11.713265245667\t54\t5.30934387045455\t2.60403542307692\t2.70530844737762\t480\t0.000945993777959354\t0.000954585043349499\tUP\n+TPGS2\t3.3725088028\t4.11996872268405\t16.9741422758948\t43\t5.97524573363636\t2.63840351461538\t3.33684221902098\t499\t0.000950977783720121\t0.000958646959395283\tUP\n+UBR4\t3.7243931961\t3.96515294318184\t15.7224378628236\t52\t6.36193680590909\t2.98047063948718\t3.38146616642191\t483\t0.000952549545941161\t0.000959264396718188\tUP\n+SNRPD1\t4.5954885485\t3.88911403853735\t15.1252080047483\t62\t6.937094105\t3.93503569923077\t3.00205840576923\t471.5\t0.000954043925253532\t0.000959802741703754\tUP\n+TCP11L1\t0.7470556144\t2.06756474210165\t4.27482396278186\t14\t1.76379030090909\t0.460284292564103\t1.30350600834499\t618\t0.000955588977383056\t0.000960390932043272\tUP\n+GPI\t8.0150228998\t3.7804567369532\t14.2918531399748\t87\t10.0335109368182\t7.44570576115385\t2.58780517566434\t461\t0.000957030077022157\t0.000960873571307387\tUP\n+SYT11\t6.453726998\t3.93503133479676\t15.4844716058324\t81\t8.67547726090909\t5.82707948794872\t2.84839777296037\t462\t0.00095916774316256\t0.000962053904877192\tUP\n+ZFAND6\t3.7815824864\t3.85685274330171\t14.8753130835139\t54\t6.11907842363636\t3.12228876051282\t2.99678966312354\t480.5\t0.000960923342587531\t0.000962849040668869\tUP\n+KIAA1468\t1.1660888359\t2.43070154440245\t5.90830999796044\t21\t2.68776202954545\t0.736898960769231\t1.95086306877622\t575\t0.000962255120989689\t0.000963218339329018\tUP\n+TMSB10\t8.0990057985\t3.69531326653996\t13.6553401378663\t90\t10.3699553059091\t7.45848157846154\t2.91147372744755\t461\t0.000963790732712819\t0.000963790732712819\tUP\n' |
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/result_from_csv.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result_from_csv.tsv Thu Nov 30 02:03:53 2023 +0000 |
| b |
| b'@@ -0,0 +1,1001 @@\n+genes\tmean\tSD\tVariance\tPercentage_Detection\tmean_condition2\tmean_condition1\tlog2FC\tstatistic\tp.value\tp.adjust\tSignificant\n+CHTOP\t3.8234613519\t3.84537289419585\t14.7868926954161\t55\t7.93857243409091\t2.66278899538462\t5.27578343870629\t221\t2.77104282187417e-08\t1.38552141093708e-05\tUP\n+GALNS\t2.2481162207\t3.51579961231222\t12.3608469139348\t32\t6.08584531863636\t1.16567980846154\t4.92016551017482\t298.5\t1.93694184665631e-08\t1.38552141093708e-05\tUP\n+ACAD9\t3.6175666278\t3.92373892857361\t15.395727179604\t50\t7.65313508727273\t2.47932937\t5.17380571727273\t252.5\t7.38169087242701e-08\t1.70542874108158e-05\tUP\n+PPP1CA\t5.5439969757\t4.24633823493944\t18.0313884055086\t68\t9.56443781545454\t4.4100264824359\t5.15441133301865\t216\t5.71634864068665e-08\t1.70542874108158e-05\tUP\n+QSOX1\t1.4023561952\t2.80910384050578\t7.89106438674434\t23\t4.37727818863636\t0.563275632948718\t3.81400255568765\t383\t8.52714370540792e-08\t1.70542874108158e-05\tUP\n+CALR\t6.1332206259\t3.74330853958279\t14.0123588225134\t82\t9.46178946409091\t5.19439351769231\t4.2673959463986\t228\t1.49386785685187e-07\t2.13409693835981e-05\tUP\n+STT3A\t5.236738824\t3.62605148242273\t13.1482493531801\t73\t8.46855458454545\t4.32520104538462\t4.14335353916084\t230\t1.33870514441858e-07\t2.13409693835981e-05\tUP\n+CHUK\t0.8719910028\t2.46162223204938\t6.05958401331976\t13\t3.16185595909091\t0.226131656153846\t2.93572430293706\t497\t2.85188510211347e-07\t3.56485637764184e-05\tUP\n+CPNE4\t0.526141333\t1.86358339179453\t3.47294305817242\t9\t2.32411542863636\t0.0190204342307692\t2.30509499440559\t553\t3.32791497459475e-07\t3.69768330510528e-05\tUP\n+CDKN2A\t7.6964229078\t3.10484757262992\t9.6400784492659\t92\t10.2291212545455\t6.98207209205128\t3.24704916249417\t248\t3.91842117256886e-07\t3.91842117256886e-05\tUP\n+LPHN2\t0.651253002\t2.13715406340722\t4.56742749073799\t9\t2.65581755227273\t0.0858630006410256\t2.5699545516317\t557\t4.73339607180964e-07\t4.30308733800876e-05\tUP\n+BOD1\t3.1497567495\t3.83739924686455\t14.7256329798366\t43\t6.73838572045454\t2.1375793474359\t4.60080637301865\t320\t7.2464212338475e-07\t5.17325024039576e-05\tUP\n+L3MBTL4\t0.9526289915\t2.43611634678434\t5.93466285506989\t16\t3.04302798727273\t0.36302927474359\t2.67999871252914\t478.5\t7.75987536059364e-07\t5.17325024039576e-05\tUP\n+RAB11FIP2\t1.1953109236\t2.4244277791648\t5.87785005638597\t22\t3.54252472954545\t0.533276260384615\t3.00924846916084\t424.5\t6.68529681059636e-07\t5.17325024039576e-05\tUP\n+TMED2\t4.8793516487\t4.43931839493608\t19.7075478116179\t58\t8.71889055227273\t3.79640477846154\t4.92248577381119\t286\t7.73621573695859e-07\t5.17325024039576e-05\tUP\n+CDC23\t1.4845877429\t2.93586935370758\t8.61932886203936\t23\t4.03794072045455\t0.764411262051282\t3.27352945840326\t422\t8.85938244801212e-07\t5.42768494562811e-05\tUP\n+KPNA6\t4.2484375509\t3.96585005887565\t15.727966689484\t60\t7.92728396\t3.21081420474359\t4.71646975525641\t288\t9.68141352346355e-07\t5.42768494562811e-05\tUP\n+MRPS15\t3.4301327823\t3.80590294950846\t14.4848972610772\t48\t6.82621584818182\t2.47226319961538\t4.35395264856643\t312\t9.76983290213059e-07\t5.42768494562811e-05\tUP\n+P4HB\t6.4598457483\t4.16631767129325\t17.3582029381304\t75\t9.84999056590909\t5.50365105615385\t4.34633950975524\t279\t1.22440375342796e-06\t6.1220187671398e-05\tUP\n+PDIA3\t5.8247363125\t3.87278033056344\t14.9984274887991\t78\t9.02030213909091\t4.92342287423077\t4.09687926486014\t277\t1.19671614202614e-06\t6.1220187671398e-05\tUP\n+GUK1\t7.5341423268\t3.66254878000738\t13.4142635659336\t86\t10.2908856654545\t6.75659933384615\t3.53428633160839\t281\t1.55859949560046e-06\t7.08454316182027e-05\tUP\n+NIPSNAP1\t1.5822353837\t3.00392732829468\t9.02357939367564\t25\t4.27341426090909\t0.823184931153846\t3.45022932975524\t418.5\t1.55424820873594e-06\t7.08454316182027e-05\tUP\n+ATL3\t1.684943722\t3.06419654740369\t9.38930048112069\t28\t4.27152092409091\t0.955396306025641\t3.31612461806527\t406.5\t2.13583627347771e-06\t7.35991999095773e-05\tUP\n+AXL\t1.8516205135\t2.99984696420088\t8.99908180862526\t33\t4.53106485\t1.09587980320513\t3.43518504679487\t380\t2.02019519292425e-06\t7.35991999095773e-05\tUP\n+C20orf27\t2.2550394962\t3.30651005019324\t10.9330087120289\t35\t5.24810855863636\t1.41084052987179\t3.83'..b'3197307692\t2.15180041132867\t610\t0.000915771581669754\t0.000938290554989502\tUP\n+VTI1A\t0.918271115\t2.40141254119344\t5.76678219300114\t15\t2.60313627136364\t0.443052737564103\t2.16008353379953\t610\t0.000915771581669754\t0.000938290554989502\tUP\n+NUP62\t2.9233171576\t3.70711604126724\t13.7427093434209\t43\t5.35756743454545\t2.23673374615385\t3.12083368839161\t498\t0.000920215840387792\t0.000941879058738784\tUP\n+DIABLO\t3.7530156708\t4.11035117966103\t16.8949868201408\t50\t6.38383409136364\t3.0109899624359\t3.37284412892774\t485\t0.000921429874995332\t0.000942157336396045\tUP\n+DOCK1\t1.0103905969\t2.34412722793681\t5.49493246075471\t19\t2.82872530454545\t0.497526961410256\t2.3311983431352\t585\t0.000924992572007006\t0.00094386997143572\tUP\n+WDR41\t2.5437584238\t3.45241040356169\t11.919137594621\t40\t4.47408604136364\t1.99930704448718\t2.47477899687646\t505\t0.000924513499482298\t0.00094386997143572\tUP\n+FIBP\t4.8655737859\t3.99732726063749\t15.9786252286356\t64\t7.44026504590909\t4.1393788151282\t3.30088623078089\t469\t0.000930327619459469\t0.000946416703417568\tUP\n+PRDX2\t5.7032473587\t4.17744859763615\t17.4510767858922\t70\t8.01002814454545\t5.05261688064103\t2.95741126390443\t465\t0.000929870174709466\t0.000946416703417568\tUP\n+SHC1\t5.8777250291\t3.80971249390208\t14.5139092861936\t77\t8.27128381863636\t5.20261870384615\t3.06866511479021\t462\t0.000929326998154864\t0.000946416703417568\tUP\n+FRS3\t0.4746996647\t1.53251529999738\t2.34860314472606\t9\t1.39806345772727\t0.214263723076923\t1.18379973465035\t660\t0.000931672286839587\t0.000946821429715027\tUP\n+COPZ1\t4.8018366619\t4.07769758494424\t16.6276175942601\t62\t7.37968796181818\t4.07475039782051\t3.30493756399767\t471\t0.000939584042631959\t0.000951959516344437\tUP\n+MRPL24\t3.0131018049\t3.6185920836997\t13.0942086682141\t44\t5.21605900772727\t2.39175490153846\t2.82430410618881\t496.5\t0.000938674990049157\t0.000951959516344437\tUP\n+PSAP\t8.5924321321\t3.44981991233812\t11.9012574275646\t92\t10.5277436009091\t8.04657505115385\t2.48116854975524\t460\t0.000938309531697593\t0.000951959516344437\tUP\n+APPL1\t2.5947342267\t3.45335825941766\t11.9256832678882\t39\t4.67491950090909\t2.00801530320513\t2.66690419770396\t508\t0.000941000129450867\t0.000952301553157109\tUP\n+POM121\t4.9834764401\t3.10875721757676\t9.66437143783559\t83\t6.75950544954545\t4.48254518102564\t2.27696026851981\t461\t0.000941826236072381\t0.000952301553157109\tUP\n+TAF10\t4.8993251071\t3.53777356074795\t12.5158417671272\t71\t7.01148492636364\t4.30358772217949\t2.70789720418415\t465\t0.000944740437866639\t0.000954283270572363\tUP\n+THBS3\t3.1992032815\t3.42246479100473\t11.713265245667\t54\t5.30934387045455\t2.60403542307692\t2.70530844737762\t480\t0.000945993777959354\t0.000954585043349499\tUP\n+TPGS2\t3.3725088028\t4.11996872268405\t16.9741422758948\t43\t5.97524573363636\t2.63840351461538\t3.33684221902098\t499\t0.000950977783720121\t0.000958646959395283\tUP\n+UBR4\t3.7243931961\t3.96515294318184\t15.7224378628236\t52\t6.36193680590909\t2.98047063948718\t3.38146616642191\t483\t0.000952549545941161\t0.000959264396718188\tUP\n+SNRPD1\t4.5954885485\t3.88911403853735\t15.1252080047483\t62\t6.937094105\t3.93503569923077\t3.00205840576923\t471.5\t0.000954043925253532\t0.000959802741703754\tUP\n+TCP11L1\t0.7470556144\t2.06756474210165\t4.27482396278186\t14\t1.76379030090909\t0.460284292564103\t1.30350600834499\t618\t0.000955588977383056\t0.000960390932043272\tUP\n+GPI\t8.0150228998\t3.7804567369532\t14.2918531399748\t87\t10.0335109368182\t7.44570576115385\t2.58780517566434\t461\t0.000957030077022157\t0.000960873571307387\tUP\n+SYT11\t6.453726998\t3.93503133479676\t15.4844716058324\t81\t8.67547726090909\t5.82707948794872\t2.84839777296037\t462\t0.00095916774316256\t0.000962053904877192\tUP\n+ZFAND6\t3.7815824864\t3.85685274330171\t14.8753130835139\t54\t6.11907842363636\t3.12228876051282\t2.99678966312354\t480.5\t0.000960923342587531\t0.000962849040668869\tUP\n+KIAA1468\t1.1660888359\t2.43070154440245\t5.90830999796044\t21\t2.68776202954545\t0.736898960769231\t1.95086306877622\t575\t0.000962255120989689\t0.000963218339329018\tUP\n+TMSB10\t8.0990057985\t3.69531326653996\t13.6553401378663\t90\t10.3699553059091\t7.45848157846154\t2.91147372744755\t461\t0.000963790732712819\t0.000963790732712819\tUP\n' |
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/signature_2columns.tsv --- a/test-data/signature_2columns.tsv Thu Aug 29 05:35:04 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,101 +0,0 @@ -cell rate -1001000173.B4 LOW -1001000173.A2 LOW -1001000173.E2 LOW -1001000173.F6 LOW -1001000173.B12 LOW -1001000173.H1 HIGH -1001000173.E4 HIGH -1001000173.C2 LOW -1001000173.F4 LOW -1001000173.E10 HIGH -1001000173.E6 LOW -1001000173.C4 HIGH -1001000173.B10 LOW -1001000173.A7 LOW -1001000173.B8 LOW -1001000173.F9 LOW -1001000173.G6 HIGH -1001000173.A9 LOW -1001000173.D2 HIGH -1001000173.F2 LOW -1001000173.H9 LOW -1001000173.G1 LOW -1001000173.B3 LOW -1001000173.D7 HIGH -1001000173.A12 LOW -1001000173.C1 LOW -1001000173.H7 HIGH -1001000173.H5 LOW -1001000173.G2 LOW -1001000173.A3 LOW -1001000173.D3 LOW -1001000173.E1 LOW -1001000173.G12 HIGH -1001000173.C10 HIGH -1001000173.C3 LOW -1001000173.A5 LOW -1001000173.G4 LOW -1001000173.B11 LOW -1001000173.G9 HIGH -1001000173.F1 LOW -1001000173.D8 LOW -1001000173.E12 HIGH -1001000173.F11 LOW -1001000173.E5 LOW -1001000173.G10 LOW -1001000173.B9 LOW -1001000173.C7 HIGH -1001000173.B2 LOW -1001000173.H4 LOW -1001000174.G5 LOW -1001000174.H9 LOW -1001000174.A10 LOW -1001000174.G10 HIGH -1001000174.C8 LOW -1001000174.F6 LOW -1001000174.B4 LOW -1001000174.H7 LOW -1001000174.E10 HIGH -1001000174.D5 LOW -1001000174.E5 LOW -1001000174.B11 LOW -1001000174.F10 LOW -1001000174.A5 LOW -1001000174.B8 LOW -1001000174.F2 LOW -1001000174.F9 HIGH -1001000174.F4 HIGH -1001000174.B6 LOW -1001000174.E2 LOW -1001000174.G2 LOW -1001000174.D8 LOW -1001000174.H6 LOW -1001000174.C3 HIGH -1001000174.B7 LOW -1001000174.A7 LOW -1001000174.H10 LOW -1001000174.F7 HIGH -1001000174.A2 LOW -1001000174.E4 LOW -1001000174.D12 LOW -1001000174.H4 LOW -1001000174.C5 LOW -1001000174.E9 LOW -1001000174.D1 LOW -1001000174.G4 LOW -1001000174.G9 LOW -1001000174.D4 HIGH -1001000174.H11 HIGH -1001000174.A9 LOW -1001000174.A4 HIGH -1001000174.C7 LOW -1001000174.D11 LOW -1001000174.F5 LOW -1001000174.G6 LOW -1001000174.D6 LOW -1001000174.H3 LOW -1001000174.F12 LOW -1001000174.E6 LOW -1001000174.G3 LOW -1001000174.A8 LOW |
| b |
| diff -r 3d86c89f15bf -r 6916ac5a9ef0 test-data/signature_3columns.tsv --- a/test-data/signature_3columns.tsv Thu Aug 29 05:35:04 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,101 +0,0 @@ -cells factor add_column -1001000173.B4 LOW 1001000173.B4 -1001000173.A2 LOW 1001000173.A2 -1001000173.E2 LOW 1001000173.E2 -1001000173.F6 LOW 1001000173.F6 -1001000173.B12 LOW 1001000173.B12 -1001000173.H1 HIGH 1001000173.H1 -1001000173.E4 HIGH 1001000173.E4 -1001000173.C2 LOW 1001000173.C2 -1001000173.F4 LOW 1001000173.F4 -1001000173.E10 HIGH 1001000173.E10 -1001000173.E6 LOW 1001000173.E6 -1001000173.C4 HIGH 1001000173.C4 -1001000173.B10 LOW 1001000173.B10 -1001000173.A7 LOW 1001000173.A7 -1001000173.B8 LOW 1001000173.B8 -1001000173.F9 LOW 1001000173.F9 -1001000173.G6 HIGH 1001000173.G6 -1001000173.A9 LOW 1001000173.A9 -1001000173.D2 HIGH 1001000173.D2 -1001000173.F2 LOW 1001000173.F2 -1001000173.H9 LOW 1001000173.H9 -1001000173.G1 LOW 1001000173.G1 -1001000173.B3 LOW 1001000173.B3 -1001000173.D7 HIGH 1001000173.D7 -1001000173.A12 LOW 1001000173.A12 -1001000173.C1 LOW 1001000173.C1 -1001000173.H7 HIGH 1001000173.H7 -1001000173.H5 LOW 1001000173.H5 -1001000173.G2 LOW 1001000173.G2 -1001000173.A3 LOW 1001000173.A3 -1001000173.D3 LOW 1001000173.D3 -1001000173.E1 LOW 1001000173.E1 -1001000173.G12 HIGH 1001000173.G12 -1001000173.C10 HIGH 1001000173.C10 -1001000173.C3 LOW 1001000173.C3 -1001000173.A5 LOW 1001000173.A5 -1001000173.G4 LOW 1001000173.G4 -1001000173.B11 LOW 1001000173.B11 -1001000173.G9 HIGH 1001000173.G9 -1001000173.F1 LOW 1001000173.F1 -1001000173.D8 LOW 1001000173.D8 -1001000173.E12 HIGH 1001000173.E12 -1001000173.F11 LOW 1001000173.F11 -1001000173.E5 LOW 1001000173.E5 -1001000173.G10 LOW 1001000173.G10 -1001000173.B9 LOW 1001000173.B9 -1001000173.C7 HIGH 1001000173.C7 -1001000173.B2 LOW 1001000173.B2 -1001000173.H4 LOW 1001000173.H4 -1001000174.G5 LOW 1001000174.G5 -1001000174.H9 LOW 1001000174.H9 -1001000174.A10 LOW 1001000174.A10 -1001000174.G10 HIGH 1001000174.G10 -1001000174.C8 LOW 1001000174.C8 -1001000174.F6 LOW 1001000174.F6 -1001000174.B4 LOW 1001000174.B4 -1001000174.H7 LOW 1001000174.H7 -1001000174.E10 HIGH 1001000174.E10 -1001000174.D5 LOW 1001000174.D5 -1001000174.E5 LOW 1001000174.E5 -1001000174.B11 LOW 1001000174.B11 -1001000174.F10 LOW 1001000174.F10 -1001000174.A5 LOW 1001000174.A5 -1001000174.B8 LOW 1001000174.B8 -1001000174.F2 LOW 1001000174.F2 -1001000174.F9 HIGH 1001000174.F9 -1001000174.F4 HIGH 1001000174.F4 -1001000174.B6 LOW 1001000174.B6 -1001000174.E2 LOW 1001000174.E2 -1001000174.G2 LOW 1001000174.G2 -1001000174.D8 LOW 1001000174.D8 -1001000174.H6 LOW 1001000174.H6 -1001000174.C3 HIGH 1001000174.C3 -1001000174.B7 LOW 1001000174.B7 -1001000174.A7 LOW 1001000174.A7 -1001000174.H10 LOW 1001000174.H10 -1001000174.F7 HIGH 1001000174.F7 -1001000174.A2 LOW 1001000174.A2 -1001000174.E4 LOW 1001000174.E4 -1001000174.D12 LOW 1001000174.D12 -1001000174.H4 LOW 1001000174.H4 -1001000174.C5 LOW 1001000174.C5 -1001000174.E9 LOW 1001000174.E9 -1001000174.D1 LOW 1001000174.D1 -1001000174.G4 LOW 1001000174.G4 -1001000174.G9 LOW 1001000174.G9 -1001000174.D4 HIGH 1001000174.D4 -1001000174.H11 HIGH 1001000174.H11 -1001000174.A9 LOW 1001000174.A9 -1001000174.A4 HIGH 1001000174.A4 -1001000174.C7 LOW 1001000174.C7 -1001000174.D11 LOW 1001000174.D11 -1001000174.F5 LOW 1001000174.F5 -1001000174.G6 LOW 1001000174.G6 -1001000174.D6 LOW 1001000174.D6 -1001000174.H3 LOW 1001000174.H3 -1001000174.F12 LOW 1001000174.F12 -1001000174.E6 LOW 1001000174.E6 -1001000174.G3 LOW 1001000174.G3 -1001000174.A8 LOW 1001000174.A8 |