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annotate dexseq.R @ 7:62adf13b86ea draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
author iuc
date Fri, 19 Mar 2021 09:45:03 +0000
parents 278b189248cd
children df929f257179
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1 ## Setup R error handling to go to stderr
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2 options(show.error.messages = F, error = function() {
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3 cat(geterrmessage(), file = stderr()); q("no", 1, F)
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4 })
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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6 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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8 suppressPackageStartupMessages({
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9 library("DEXSeq")
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10 library("getopt")
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11 library("rjson")
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12 })
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15 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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16 args <- commandArgs(trailingOnly = TRUE)
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18 #get options, using the spec as defined by the enclosed list.
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19 #we read the options from the default: commandArgs(TRUE).
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20 spec <- matrix(c(
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21 "verbose", "v", 2, "integer",
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22 "help", "h", 0, "logical",
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23 "gtf", "a", 1, "character",
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24 "outfile", "o", 1, "character",
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25 "reportdir", "r", 1, "character",
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26 "rds", "d", 1, "character",
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27 "factors", "f", 1, "character",
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28 "threads", "p", 1, "integer",
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29 "fdr", "c", 1, "double"
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30 ), byrow = TRUE, ncol = 4);
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31 opt <- getopt(spec);
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33 # if help was asked for print a friendly message
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34 # and exit with a non-zero error code
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35 if (!is.null(opt$help)) {
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36 cat(getopt(spec, usage = TRUE));
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37 q(status = 1);
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38 }
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39
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40 trim <- function(x) gsub("^\\s+|\\s+$", "", x)
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41 opt$samples <- trim(opt$samples)
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42 opt$factors <- trim(opt$factors)
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44 parser <- newJSONParser()
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45 parser$addData(opt$factors)
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46 factors_list <- parser$getObject()
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48 sample_table <- data.frame()
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49 count_files <- c()
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50 factor_names <- c()
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51 primary_factor <- ""
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52 for (factor in factors_list) {
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53 factor_name <- factor[[1]]
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54 factor_names <- append(factor_names, paste(factor_name, "exon", sep = ":"))
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55 factor_values_map_list <- factor[[2]]
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56 c <- length(factor_values_map_list)
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57 for (factorValuesMap in factor_values_map_list) {
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58 for (files in factorValuesMap) {
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59 for (file in files) {
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60 if (primary_factor == "") {
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61 count_files <- append(count_files, file)
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62 }
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63 sample_table[basename(file), factor_name] <- paste(c, names(factorValuesMap), sep = "_")
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64 }
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65 }
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66 c <- c - 1
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67 }
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68 if (primary_factor == "") {
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69 primary_factor <- factor_name
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70 }
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71 }
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73 factor_names <- append(factor_names, "exon")
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74 factor_names <- append(factor_names, "sample")
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75 factor_names <- rev(factor_names)
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76 formula_full_model <- as.formula(paste("", paste(factor_names, collapse = " + "), sep = " ~ "))
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77 factor_names <- head(factor_names, -1)
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78 formula_reduced_model <- as.formula(paste("", paste(factor_names, collapse = " + "), sep = " ~ "))
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80 sample_table
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81 formula_full_model
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82 formula_reduced_model
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83 primary_factor
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84 count_files
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85 opt$reportdir
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86 opt$threads
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87 getwd()
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89 dxd <- DEXSeqDataSetFromHTSeq(count_files, sampleData = sample_table, design = formula_full_model, flattenedfile = opt$gtf)
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90
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91 colData(dxd)
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92 dxd <- estimateSizeFactors(dxd)
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93 print("Estimated size factors")
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94 sizeFactors(dxd)
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95 bpparam <- MulticoreParam(workers = opt$threads)
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96 dxd <- estimateDispersions(dxd, formula = formula_full_model, BPPARAM = bpparam)
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97 print("Estimated dispersions")
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98 dxd <- testForDEU(dxd, reducedModel = formula_reduced_model, fullModel = formula_full_model, BPPARAM = bpparam)
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99 print("tested for DEU")
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100 dxd <- estimateExonFoldChanges(dxd, fitExpToVar = primary_factor, BPPARAM = bpparam)
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101 print("Estimated fold changes")
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102 res <- DEXSeqResults(dxd)
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103 print("Results")
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104 table(res$padj <= opt$fdr)
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105 res_sorted <- res[order(res$padj), ]
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106 head(res_sorted)
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107
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108 export_table <- as.data.frame(res_sorted)
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109 last_column <- ncol(export_table)
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110 for (i in seq_len(nrow(export_table))) {
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111 export_table[i, last_column] <- paste(export_table[i, last_column][[1]], collapse = ", ")
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112 }
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113 write.table(export_table, file = opt$outfile, sep = "\t", quote = FALSE, col.names = FALSE)
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114 print("Written Results")
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115
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116 if (!is.null(opt$rds)) {
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117 saveRDS(res, file = "DEXSeqResults.rds")
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118 }
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119
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120 if (!is.null(opt$reportdir)) {
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121 DEXSeqHTML(res, fitExpToVar = primary_factor, path = opt$reportdir, FDR = opt$fdr, color = c("#B7FEA0", "#FF8F43", "#637EE9", "#FF0000", "#F1E7A1", "#C3EEE7", "#CEAEFF", "#EDC3C5", "#AAA8AA"))
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122 }
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123 sessionInfo()