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annotate diffbind.R @ 17:2605cbdaa7d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 3da34ac6e5b18fd5deacaf31b757aca6bae82251
author iuc
date Fri, 15 Dec 2023 19:39:14 +0000
parents 163688bb8f73
children f907216064f6
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1 ## Setup R error handling to go to stderr
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2 options(show.error.messages = FALSE, error = function() {
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3 cat(geterrmessage(), file = stderr())
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4 q("no", 1, FALSE)
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5 })
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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7 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 suppressPackageStartupMessages({
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10 library("getopt")
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11 library("DiffBind")
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12 library("rjson")
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13 })
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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 "infile", "i", 1, "character",
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22 "outfile", "o", 1, "character",
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23 "scorecol", "n", 1, "integer",
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24 "lowerbetter", "l", 1, "logical",
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25 "summits", "s", 1, "integer",
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26 "th", "t", 1, "double",
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27 "format", "f", 1, "character",
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28 "plots", "p", 2, "character",
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29 "bmatrix", "b", 0, "logical",
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30 "rdaOpt", "r", 0, "logical",
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31 "infoOpt", "a", 0, "logical",
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32 "verbose", "v", 2, "integer",
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33 "help", "h", 0, "logical"
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34 ), byrow = TRUE, ncol = 4)
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35
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36 opt <- getopt(spec)
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38 # if help was asked for print a friendly message
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39 # and exit with a non-zero error code
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40 if (!is.null(opt$help)) {
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41 cat(getopt(spec, usage = TRUE))
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42 q(status = 1)
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43 }
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45 parser <- newJSONParser()
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46 parser$addData(opt$infile)
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47 factor_list <- parser$getObject()
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48 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
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49 peaks <- filenames_in[grepl("peaks.bed", filenames_in)]
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50 bams <- filenames_in[grepl("bamreads.bam", filenames_in)]
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51 ctrls <- filenames_in[grepl("bamcontrol.bam", filenames_in)]
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53 # get the group and sample id from the peaks filenames
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54 groups <- sapply(strsplit(peaks, "-"), `[`, 1)
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55 samples <- sapply(strsplit(peaks, "-"), `[`, 2)
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57 if (length(ctrls) != 0) {
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58 sample_table <- data.frame(
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59 SampleID = samples,
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60 Condition = groups,
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61 bamReads = bams,
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62 bamControl = ctrls,
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63 Peaks = peaks,
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64 Tissue = samples
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65 ) # using "Tissue" column to display ids as labels in PCA plot
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66 } else {
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67 sample_table <- data.frame(
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68 SampleID = samples,
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69 Replicate = samples,
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70 Condition = groups,
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71 bamReads = bams,
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72 Peaks = peaks,
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73 Tissue = samples
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74 )
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75 }
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77 sample <- dba(sampleSheet = sample_table, peakFormat = "bed", scoreCol = opt$scorecol, bLowerScoreBetter = opt$lowerbetter)
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79 if (!is.null(opt$summits)) {
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80 sample_count <- dba.count(sample, summits = opt$summits)
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81 } else {
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82 sample_count <- dba.count(sample)
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83 }
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84
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85 sample_contrast <- dba.contrast(sample_count, categories = DBA_CONDITION, minMembers = 2)
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86 sample_analyze <- dba.analyze(sample_contrast)
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87 diff_bind <- dba.report(sample_analyze, th = opt$th)
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88
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89 # Generate plots
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90 if (!is.null(opt$plots)) {
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91 pdf(opt$plots)
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92 orvals <- dba.plotHeatmap(sample_analyze, contrast = 1, correlations = FALSE, cexCol = 0.8, th = opt$th)
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93 dba.plotPCA(sample_analyze, contrast = 1, th = opt$th, label = DBA_TISSUE, labelSize = 0.3)
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94 dba.plotMA(sample_analyze, th = opt$th)
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95 dba.plotVolcano(sample_analyze, th = opt$th)
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96 dba.plotBox(sample_analyze, th = opt$th)
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97 dev.off()
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98 }
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99
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100 # Output differential binding sites
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101 res_sorted <- diff_bind[order(diff_bind$FDR), ]
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102 # Convert from GRanges (1-based) to 0-based format (adapted from https://www.biostars.org/p/89341/)
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103 if (opt$format == "bed") {
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104 res_sorted <- data.frame(
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105 Chrom = seqnames(res_sorted),
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106 Start = start(res_sorted) - 1,
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107 End = end(res_sorted),
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108 Name = rep("DiffBind", length(res_sorted)),
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109 Score = rep("0", length(res_sorted)),
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110 Strand = gsub("\\*", ".", strand(res_sorted))
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111 )
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112 } else if (opt$format == "interval") {
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113 # Output as interval
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114 df <- as.data.frame(res_sorted)
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115 extrainfo <- NULL
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116 for (i in seq_len(nrow(df))) {
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117 extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse = "|")
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118 }
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119 res_sorted <- data.frame(
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120 Chrom = seqnames(res_sorted),
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121 Start = start(res_sorted) - 1,
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122 End = end(res_sorted),
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123 Name = rep("DiffBind", length(res_sorted)),
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124 Score = rep("0", length(res_sorted)),
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125 Strand = gsub("\\*", ".", strand(res_sorted)),
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126 Comment = extrainfo
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127 )
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128 } else {
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129 # Output as 0-based tabular
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130 res_sorted <- data.frame(
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131 Chrom = seqnames(res_sorted),
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132 Start = start(res_sorted) - 1,
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133 End = end(res_sorted),
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134 Name = rep("DiffBind", length(res_sorted)),
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135 Score = rep("0", length(res_sorted)),
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136 Strand = gsub("\\*", ".", strand(res_sorted)),
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137 mcols(res_sorted)
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138 )
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139 }
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140 write.table(res_sorted, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE)
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141
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142 # Output binding affinity scores
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143 if (!is.null(opt$bmatrix)) {
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144 bmat <- dba.peakset(sample_count, bRetrieve = TRUE, DataType = DBA_DATA_FRAME)
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145 # Output as 0-based tabular
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146 bmat <- data.frame(
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147 Chrom = bmat[, 1],
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148 Start = bmat[, 2] - 1,
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149 End = bmat[, 3],
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150 bmat[, 4:ncol(bmat)]
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151 )
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152 write.table(bmat, file = "bmatrix.tab", sep = "\t", quote = FALSE, row.names = FALSE)
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153 }
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154
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155 # Output RData file
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156 if (!is.null(opt$rdaOpt)) {
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157 save.image(file = "DiffBind_analysis.RData")
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158 }
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159
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160 # Output analysis info
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161 if (!is.null(opt$infoOpt)) {
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162 info <- "DiffBind_analysis_info.txt"
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163 cat("dba.count Info\n\n", file = info, append = TRUE)
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164 capture.output(sample, file = info, append = TRUE)
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165 cat("\ndba.analyze Info\n\n", file = info, append = TRUE)
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166 capture.output(sample_analyze, file = info, append = TRUE)
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167 cat("\nSessionInfo\n\n", file = info, append = TRUE)
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168 capture.output(sessionInfo(), file = info, append = TRUE)
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169 }