Mercurial > repos > rnateam > chipseeker

annotate chipseeker.R @ 7:e23396bf7bdb draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
author rnateam
date Fri, 27 Aug 2021 10:50:18 +0000
parents 7da70e9119b2
children
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7
e23396bf7bdb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit d30c91c3b4f71ec45b72976f7c2f08ea7df1e376-dirty"
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1 options(
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2 show.error.messages = F,
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3 error = function() {
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4 cat(geterrmessage(), file = stderr())
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5 q("no", 1, F)
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6 }
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7 )
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8
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9 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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11
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12 suppressPackageStartupMessages({
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13 library(ChIPseeker)
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14 library(GenomicFeatures)
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15 library(rtracklayer)
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16 library(optparse)
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17 library(ggupset)
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18 })
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19
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20 option_list <- list(
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21 make_option(c("-i", "--infile"), type = "character", help = "Peaks file to be annotated"),
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22 make_option(c("-H", "--header"), type = "logical", help = "Peaks file contains header row"),
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23 make_option(c("-G", "--gtf"), type = "character", help = "GTF to create TxDb."),
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24 make_option(c("-u", "--upstream"), type = "integer", help = "TSS upstream region"),
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25 make_option(c("-d", "--downstream"), type = "integer", help = "TSS downstream region"),
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26 make_option(c("-F", "--flankgeneinfo"), type = "logical", help = "Add flanking gene info"),
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27 make_option(c("-D", "--flankgenedist"), type = "integer", help = "Flanking gene distance"),
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28 make_option(c("-j", "--ignore_upstream"), type = "logical", help = "Ignore upstream"),
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29 make_option(
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30 c("-k", "--ignore_downstream"),
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31 type = "logical",
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32 help = "Ignore downstream"
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33 ),
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34 make_option(c("-f", "--format"), type = "character", help = "Output format (interval or tabular)."),
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35 make_option(c("-p", "--plots"), type = "logical", help = "PDF of plots."),
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36 make_option(c("-r", "--rdata"), type = "logical", help = "Output RData file.")
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37 )
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38
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39 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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40 args <- parse_args(parser)
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41
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42 peaks <- args$infile
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43 gtf <- args$gtf
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44 up <- args$upstream
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45 down <- args$downstream
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46 format <- args$format
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47
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48 if (!is.null(args$flankgeneinfo)) {
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49 flankgeneinfo <- TRUE
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50 } else {
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51 flankgeneinfo <- FALSE
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52 }
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53
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54 if (!is.null(args$ignore_upstream)) {
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55 ignore_upstream <- TRUE
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56 } else {
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57 ignore_upstream <- FALSE
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58 }
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59
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60 if (!is.null(args$ignore_downstream)) {
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61 ignore_downstream <- TRUE
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62 } else {
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63 ignore_downstream <- FALSE
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64 }
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65
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66 if (!is.null(args$header)) {
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67 header <- TRUE
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68 } else {
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69 header <- FALSE
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70 }
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71
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72 peaks <- readPeakFile(peaks, header = header)
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74 # Make TxDb from GTF
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75 txdb <- makeTxDbFromGFF(gtf, format = "gtf")
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77 # Annotate peaks
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78 peak_anno <- annotatePeak(
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79 peaks,
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80 TxDb = txdb,
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81 tssRegion = c(-up, down),
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82 addFlankGeneInfo = flankgeneinfo,
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83 flankDistance = args$flankgenedist,
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84 ignoreUpstream = ignore_upstream,
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85 ignoreDownstream = ignore_downstream
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86 )
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87
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88 # Add gene name
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89 features <- import(gtf, format = "gtf")
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90 ann <- unique(mcols(features)[, c("gene_id", "gene_name")])
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91 res <- as.data.frame(peak_anno)
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92 res <- merge(res, ann, by.x = "geneId", by.y = "gene_id")
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93 names(res)[names(res) == "gene_name"] <- "geneName"
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94
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95 #Extract metadata cols, 1st is geneId, rest should be from col 7 to end
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96 metacols <- res[, c(7:ncol(res), 1)]
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97 # Convert from 1-based to 0-based format
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98 if (format == "interval") {
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99 metacols <-
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100 apply(as.data.frame(metacols), 1, function(col)
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101 paste(col, collapse = "|"))
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102 resout <- data.frame(res$seqnames,
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103 res$start - 1,
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104 res$end,
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105 metacols)
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106 colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment")
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107 } else {
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108 resout <- data.frame(res$seqnames,
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109 res$start - 1,
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110 res$end,
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111 metacols)
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112 colnames(resout)[1:3] <- c("Chrom", "Start", "End")
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113 }
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114 write.table(
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115 resout,
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116 file = "out.tab",
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117 sep = "\t",
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118 row.names = FALSE,
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119 quote = FALSE
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120 )
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121
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122 if (!is.null(args$plots)) {
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123 pdf("out.pdf", width = 14)
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124 plotAnnoPie(peak_anno)
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125 p1 <- plotAnnoBar(peak_anno)
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126 print(p1)
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127 vennpie(peak_anno)
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128 upsetplot(peak_anno)
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129 p2 <-
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130 plotDistToTSS(peak_anno, title = "Distribution of transcription factor-binding loci\nrelative to TSS")
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131 print(p2)
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132 dev.off()
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133 rm(p1, p2)
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134 }
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135
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136 ## Output RData file
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137
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138 if (!is.null(args$rdata)) {
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139 save.image(file = "ChIPseeker_analysis.RData")
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140 }