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annotate diffbind.R @ 15:194e3f2c1d86 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 515da67fc6c289aa7ea75a0819b5da3a902f87a2
author iuc
date Tue, 09 Jul 2019 18:46:09 -0400
parents 1de83981d43c
children 163688bb8f73
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1 ## Setup R error handling to go to stderr
6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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6 suppressPackageStartupMessages({
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7 library('getopt')
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8 library('DiffBind')
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9 library('rjson')
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10 })
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12 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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13 args <- commandArgs(trailingOnly = TRUE)
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6171163112de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diffbind commit 9de99de5fb4c62f889814ea43b8800ce8d28eb83
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15 #get options, using the spec as defined by the enclosed list.
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16 #we read the options from the default: commandArgs(TRUE).
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17 spec = matrix(c(
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18 'infile' , 'i', 1, "character",
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19 'outfile' , 'o', 1, "character",
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20 'scorecol', 'n', 1, "integer",
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21 'lowerbetter', 'l', 1, "logical",
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22 'summits', 's', 1, "integer",
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23 'th', 't', 1, "double",
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24 'format', 'f', 1, "character",
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25 'plots' , 'p', 2, "character",
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26 'bmatrix', 'b', 0, "logical",
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27 "rdaOpt", "r", 0, "logical",
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28 'infoOpt' , 'a', 0, "logical",
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29 'verbose', 'v', 2, "integer",
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30 'help' , 'h', 0, "logical"
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31 ), byrow=TRUE, ncol=4);
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33 opt = getopt(spec);
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35 # if help was asked for print a friendly message
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36 # and exit with a non-zero error code
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37 if ( !is.null(opt$help) ) {
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38 cat(getopt(spec, usage=TRUE));
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39 q(status=1);
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40 }
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41
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42 parser <- newJSONParser()
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43 parser$addData(opt$infile)
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44 factorList <- parser$getObject()
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45 filenamesIn <- unname(unlist(factorList[[1]][[2]]))
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46 peaks <- filenamesIn[grepl("peaks.bed", filenamesIn)]
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47 bams <- filenamesIn[grepl("bamreads.bam", filenamesIn)]
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48 ctrls <- filenamesIn[grepl("bamcontrol.bam", filenamesIn)]
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49
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50 # get the group and sample id from the peaks filenames
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51 groups <- sapply(strsplit(peaks,"-"), `[`, 1)
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52 samples <- sapply(strsplit(peaks,"-"), `[`, 2)
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54 if ( length(ctrls) != 0 ) {
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55 sampleTable <- data.frame(SampleID=samples,
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56 Condition=groups,
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57 bamReads=bams,
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58 bamControl=ctrls,
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59 Peaks=peaks,
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60 Tissue=samples) # using "Tissue" column to display ids as labels in PCA plot
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61 } else {
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63 sampleTable <- data.frame(SampleID=samples,
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64 Replicate=samples,
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65 Condition=groups,
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66 bamReads=bams,
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67 Peaks=peaks,
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68 Tissue=samples)
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69 }
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70
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71 sample = dba(sampleSheet=sampleTable, peakFormat='bed', scoreCol=opt$scorecol, bLowerScoreBetter=opt$lowerbetter)
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73 if ( !is.null(opt$summits) ) {
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74 sample_count = dba.count(sample, summits=opt$summits)
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75 } else {
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76 sample_count = dba.count(sample)
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77 }
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78
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79 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION, minMembers=2)
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80 sample_analyze = dba.analyze(sample_contrast)
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81 diff_bind = dba.report(sample_analyze, th=opt$th)
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82
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83 # Generate plots
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84 if ( !is.null(opt$plots) ) {
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85 pdf(opt$plots)
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86 orvals = dba.plotHeatmap(sample_analyze, contrast=1, correlations=FALSE, cexCol=0.8, th=opt$th)
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87 dba.plotPCA(sample_analyze, contrast=1, th=opt$th, label=DBA_TISSUE, labelSize=0.3)
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88 dba.plotMA(sample_analyze, th=opt$th)
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89 dba.plotVolcano(sample_analyze, th=opt$th)
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90 dba.plotBox(sample_analyze, th=opt$th)
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91 dev.off()
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92 }
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93
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94 # Output differential binding sites
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95 resSorted <- diff_bind[order(diff_bind$FDR),]
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96 # Convert from GRanges (1-based) to 0-based format (adapted from https://www.biostars.org/p/89341/)
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97 if (opt$format == "bed") {
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98 resSorted <- data.frame(Chrom=seqnames(resSorted),
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99 Start=start(resSorted) - 1,
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100 End=end(resSorted),
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101 Name=rep("DiffBind", length(resSorted)),
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102 Score=rep("0", length(resSorted)),
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103 Strand=gsub("\\*", ".", strand(resSorted)))
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104 } else if (opt$format == "interval") {
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105 # Output as interval
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106 df <- as.data.frame(resSorted)
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107 extrainfo <- NULL
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108 for (i in 1:nrow(df)) {
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109 extrainfo[i] <- paste0(c(df$width[i], df[i, 6:ncol(df)]), collapse="|")
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110 }
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111 resSorted <- data.frame(Chrom=seqnames(resSorted),
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112 Start=start(resSorted) - 1,
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113 End=end(resSorted),
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114 Name=rep("DiffBind", length(resSorted)),
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115 Score=rep("0", length(resSorted)),
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116 Strand=gsub("\\*", ".", strand(resSorted)),
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117 Comment=extrainfo)
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118 } else {
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119 # Output as 0-based tabular
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120 resSorted <- data.frame(Chrom=seqnames(resSorted),
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121 Start=start(resSorted) - 1,
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122 End=end(resSorted),
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123 Name=rep("DiffBind", length(resSorted)),
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124 Score=rep("0", length(resSorted)),
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125 Strand=gsub("\\*", ".", strand(resSorted)),
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126 mcols(resSorted))
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127 }
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128 write.table(resSorted, file = opt$outfile, sep="\t", quote = FALSE, row.names = FALSE)
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129
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130 # Output binding affinity scores
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131 if (!is.null(opt$bmatrix)) {
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132 bmat <- dba.peakset(sample_count, bRetrieve=TRUE, DataType=DBA_DATA_FRAME)
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133 # Output as 0-based tabular
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134 bmat <- data.frame(Chrom=bmat[, 1],
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135 Start=bmat[, 2] - 1,
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136 End=bmat[, 3],
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137 bmat[, 4:ncol(bmat)])
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138 write.table(bmat, file="bmatrix.tab", sep="\t", quote=FALSE, row.names=FALSE)
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139 }
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140
11
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141 # Output RData file
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142 if (!is.null(opt$rdaOpt)) {
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143 save.image(file = "DiffBind_analysis.RData")
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144 }
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145
11
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146 # Output analysis info
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147 if (!is.null(opt$infoOpt)) {
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148 info <- "DiffBind_analysis_info.txt"
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149 cat("dba.count Info\n\n", file=info, append = TRUE)
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150 capture.output(sample, file=info, append=TRUE)
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151 cat("\ndba.analyze Info\n\n", file=info, append = TRUE)
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152 capture.output(sample_analyze, file=info, append=TRUE)
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153 cat("\nSessionInfo\n\n", file=info, append = TRUE)
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154 capture.output(sessionInfo(), file=info, append=TRUE)
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155 }