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annotate chipseeker.R @ 7:1b9a9409831d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/chipseeker commit e07ee851144e07fde91877727d6a39a1906f7639
author rnateam
date Sat, 27 Apr 2019 11:04:35 -0400
parents b418a1d3585d
children 8bd92f2404dd
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1 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 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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6 suppressPackageStartupMessages({
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7 library(ChIPseeker)
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8 library(GenomicFeatures)
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9 library(rtracklayer)
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10 library(optparse)
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11 })
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13 option_list <- list(
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14 make_option(c("-i","--infile"), type="character", help="Peaks file to be annotated"),
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15 make_option(c("-H","--header"), type="logical", help="Peaks file contains header row"),
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16 make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."),
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17 make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"),
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18 make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"),
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19 make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"),
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20 make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"),
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21 make_option(c("-j","--ignoreUpstream"), type="logical", help="Ignore upstream"),
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22 make_option(c("-k","--ignoreDownstream"), type="logical", help="Ignore downstream"),
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23 make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."),
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24 make_option(c("-p","--plots"), type="logical", help="PDF of plots."),
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25 make_option(c("-r","--rdata"), type="logical", help="Output RData file.")
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26 )
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28 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
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29 args = parse_args(parser)
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31 peaks = args$infile
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32 gtf = args$gtf
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33 up = args$upstream
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34 down = args$downstream
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35 format = args$format
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36
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37 if (!is.null(args$flankgeneinfo)) {
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38 flankgeneinfo <- TRUE
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39 } else {
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40 flankgeneinfo <- FALSE
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41 }
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43 if (!is.null(args$ignoreUpstream)) {
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44 ignoreUpstream <- TRUE
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45 } else {
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46 ignoreUpstream <- FALSE
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47 }
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48
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49 if (!is.null(args$ignoreDownstream)) {
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50 ignoreDownstream <- TRUE
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51 } else {
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52 ignoreDownstream <- FALSE
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53 }
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54
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55 if (!is.null(args$header)) {
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56 header <- TRUE
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57 } else {
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58 header <- FALSE
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59 }
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61 peaks <- readPeakFile(peaks, header=header)
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63 # Make TxDb from GTF
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64 txdb <- makeTxDbFromGFF(gtf, format="gtf")
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66 # Annotate peaks
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67 peakAnno <- annotatePeak(peaks, TxDb=txdb,
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68 tssRegion=c(-up, down),
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69 addFlankGeneInfo=flankgeneinfo,
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70 flankDistance=args$flankgenedist,
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71 ignoreUpstream=ignoreUpstream,
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72 ignoreDownstream=ignoreDownstream)
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73
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74 # Add gene name
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75 features <- import(gtf, format="gtf")
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76 ann <- unique(mcols(features)[, c("gene_id", "gene_name")])
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77 res <- as.data.frame(peakAnno)
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78 res <- merge(res, ann, by.x="geneId", by.y="gene_id")
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79 names(res)[names(res) == "gene_name"] <- "geneName"
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80
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81 #Extract metadata cols, 1st is geneId, rest should be from col 7 to end
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82 metacols <- res[, c(7:ncol(res), 1)]
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83 # Convert from 1-based to 0-based format
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84 if (format == "interval") {
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85 metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|"))
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86 resout <- data.frame(res$seqnames,
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87 res$start - 1,
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88 res$end,
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89 metacols)
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90 colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment")
1
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91 } else {
4
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92 resout <- data.frame(res$seqnames,
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93 res$start - 1,
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94 res$end,
1
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95 metacols)
4
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96 colnames(resout)[1:3] <- c("Chrom", "Start", "End")
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97 }
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98 write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE)
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99
3
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100 if (!is.null(args$plots)) {
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101 pdf("out.pdf", width=14)
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102 plotAnnoPie(peakAnno)
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103 p1 <- plotAnnoBar(peakAnno)
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104 print(p1)
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105 vennpie(peakAnno)
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106 upsetplot(peakAnno)
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107 p2 <- plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
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108 print(p2)
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109 dev.off()
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110 rm(p1, p2)
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111 }
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112
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113 ## Output RData file
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114
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115 if (!is.null(args$rdata)) {
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116 save.image(file = "ChIPseeker_analysis.RData")
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117 }