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annotate diffbind.R @ 30:6b235ac52faf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit fd148a124034b44d0d61db3eec32ff991d8c152c
author iuc
date Mon, 08 Jul 2024 18:31:37 +0000
parents f567dc4145ac
children
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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())
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4 q("no", 1, F)
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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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17
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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 "method", "m", 1, "character",
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24 "scorecol", "n", 1, "integer",
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25 "lowerbetter", "l", 1, "logical",
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26 "summits", "s", 1, "integer",
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27 "th", "t", 1, "double",
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28 "minoverlap", "O", 1, "integer",
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29 "use_blacklist", "B", 0, "logical",
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30 "format", "f", 1, "character",
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31 "plots", "p", 2, "character",
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32 "bmatrix", "b", 0, "logical",
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33 "rdaOpt", "r", 0, "logical",
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34 "infoOpt", "a", 0, "logical",
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35 "verbose", "v", 2, "integer",
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36 "help", "h", 0, "logical"
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37 ), byrow = TRUE, ncol = 4)
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38
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39 opt <- getopt(spec)
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40 # if help was asked for print a friendly message
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41 # and exit with a non-zero error code
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42 if (!is.null(opt$help)) {
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43 cat(getopt(spec, usage = TRUE))
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44 q(status = 1)
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45 }
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46
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47 parser <- newJSONParser()
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48 parser$addData(opt$infile)
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49 factor_list <- parser$getObject()
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50 filenames_in <- unname(unlist(factor_list[[1]][[2]]))
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51 peaks <- filenames_in[grepl("peaks.bed", filenames_in)]
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52 bams <- filenames_in[grepl("bamreads.bam", filenames_in)]
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53 ctrls <- filenames_in[grepl("bamcontrol.bam", filenames_in)]
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55 # get the group and sample id from the peaks filenames
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56 groups <- sapply(strsplit(peaks, "-"), `[`, 1)
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57 samples <- sapply(strsplit(peaks, "-"), `[`, 2)
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58
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59 if (length(ctrls) != 0) {
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60 sample_table <- data.frame(
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61 SampleID = samples,
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62 Condition = groups,
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63 bamReads = bams,
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64 bamControl = ctrls,
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65 Peaks = peaks,
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66 Tissue = samples
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67 ) # using "Tissue" column to display ids as labels in PCA plot
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68 } else {
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69 sample_table <- data.frame(
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70 SampleID = samples,
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71 Replicate = samples,
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72 Condition = groups,
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73 bamReads = bams,
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74 Peaks = peaks,
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75 Tissue = samples
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76 )
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77 }
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78
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79 sample <- dba(sampleSheet = sample_table, peakFormat = "bed", scoreCol = opt$scorecol, bLowerScoreBetter = opt$lowerbetter, minOverlap = opt$minoverlap)
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80
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81 if (!is.null(opt$use_blacklist)) {
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82 sample <- dba.blacklist(sample, blacklist = TRUE)
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83 }
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84
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85 if (!is.null(opt$summits)) {
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86 sample_count <- dba.count(sample, summits = opt$summits)
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87 } else {
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88 sample_count <- dba.count(sample)
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89 }
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90
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91 sample_contrast <- dba.contrast(sample_count, categories = DBA_CONDITION, minMembers = 2)
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92
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93 if (opt$method == "DBA_DESEQ2") {
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94 method <- DBA_DESEQ2
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95 } else if (opt$method == "DBA_EDGER") {
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96 method <- DBA_EDGER
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97 }
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98
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99 sample_analyze <- dba.analyze(sample_contrast, method = method, bBlacklist = FALSE, bGreylist = FALSE)
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100
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101 diff_bind <- dba.report(sample_analyze, th = opt$th, method = method)
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102
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103 # Generate plots
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104 if (!is.null(opt$plots)) {
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105 pdf(opt$plots)
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106 orvals <- dba.plotHeatmap(sample_analyze, contrast = 1, correlations = FALSE, cexCol = 0.8, th = opt$th, method = method)
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107 dba.plotPCA(sample_analyze, contrast = 1, th = opt$th, label = DBA_TISSUE, labelSize = 0.3, method = method)
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108 dba.plotMA(sample_analyze, th = opt$th, method = method)
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109 dba.plotVolcano(sample_analyze, th = opt$th, method = method)
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110 dba.plotBox(sample_analyze, th = opt$th, method = method)
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111 dev.off()
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112 }
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113
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114 # Output differential binding sites
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115 res_sorted <- diff_bind[order(diff_bind$FDR), ]
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116 # Convert from GRanges (1-based) to 0-based format (adapted from https://www.biostars.org/p/89341/)
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117 if (opt$format == "bed") {
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118 res_sorted <- data.frame(
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119 Chrom = seqnames(res_sorted),
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120 Start = start(res_sorted) - 1,
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121 End = end(res_sorted),
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122 Name = rep("DiffBind", length(res_sorted)),
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123 Score = rep("0", length(res_sorted)),
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124 Strand = gsub("\\*", ".", strand(res_sorted))
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125 )
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126 } else if (opt$format == "interval") {
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127 # Output as interval
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128 df <- as.data.frame(res_sorted)
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129 extrainfo <- NULL
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130 for (i in seq_len(nrow(df))) {
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131 extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse = "|")
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132 }
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133 res_sorted <- data.frame(
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134 Chrom = seqnames(res_sorted),
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135 Start = start(res_sorted) - 1,
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136 End = end(res_sorted),
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137 Name = rep("DiffBind", length(res_sorted)),
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138 Score = rep("0", length(res_sorted)),
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139 Strand = gsub("\\*", ".", strand(res_sorted)),
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140 Comment = extrainfo
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141 )
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142 } else {
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143 # Output as 0-based tabular
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144 res_sorted <- data.frame(
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145 Chrom = seqnames(res_sorted),
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146 Start = start(res_sorted) - 1,
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147 End = end(res_sorted),
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148 Name = rep("DiffBind", length(res_sorted)),
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149 Score = rep("0", length(res_sorted)),
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150 Strand = gsub("\\*", ".", strand(res_sorted)),
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151 mcols(res_sorted)
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152 )
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153 }
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154 write.table(res_sorted, file = opt$outfile, sep = "\t", quote = FALSE, row.names = FALSE)
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155
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156 # Output binding affinity scores
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157 if (!is.null(opt$bmatrix)) {
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158 bmat <- dba.peakset(sample_count, bRetrieve = TRUE, DataType = DBA_DATA_FRAME, minOverlap = opt$minoverlap)
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159 # Output as 0-based tabular
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160 bmat <- data.frame(
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161 Chrom = bmat[, 1],
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162 Start = bmat[, 2] - 1,
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163 End = bmat[, 3],
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164 bmat[, 4:ncol(bmat)]
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165 )
28
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166 write.table(bmat, file = "bmatrix.tab", sep = "\t", quote = FALSE, row.names = FALSE)
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167 }
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168
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169 # Output RData file
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170 if (!is.null(opt$rdaOpt)) {
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171 save.image(file = "DiffBind_analysis.RData")
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172 }
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173
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174 # Output analysis info
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175 if (!is.null(opt$infoOpt)) {
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176 info <- "DiffBind_analysis_info.txt"
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177 cat("dba.count Info\n\n", file = info, append = TRUE)
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178 capture.output(sample, file = info, append = TRUE)
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179 cat("\ndba.analyze Info\n\n", file = info, append = TRUE)
f567dc4145ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents: 27
diff changeset
180 capture.output(sample_analyze, file = info, append = TRUE)
f567dc4145ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents: 27
diff changeset
181 cat("\nSessionInfo\n\n", file = info, append = TRUE)
f567dc4145ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents: 27
diff changeset
182 capture.output(sessionInfo(), file = info, append = TRUE)
f567dc4145ac "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 77828512472bf9815bdda725a58a2321f7803661"
iuc
parents: 27
diff changeset
183 }