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annotate chipseeker.R @ 5:3ff6333973aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
author rnateam
date Wed, 13 Mar 2019 03:06:39 -0400
parents a6d072a82158
children 7da70e9119b2
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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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1 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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4 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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6 suppressPackageStartupMessages({
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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7 library(ChIPseeker)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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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 })
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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13 option_list <- list(
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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14 make_option(c("-i","--infile"), type="character", help="Peaks file to be annotated"),
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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15 make_option(c("-G","--gtf"), type="character", help="GTF to create TxDb."),
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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16 make_option(c("-u","--upstream"), type="integer", help="TSS upstream region"),
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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17 make_option(c("-d","--downstream"), type="integer", help="TSS downstream region"),
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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18 make_option(c("-F","--flankgeneinfo"), type="logical", help="Add flanking gene info"),
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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19 make_option(c("-D","--flankgenedist"), type="integer", help="Flanking gene distance"),
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20 make_option(c("-j","--ignoreUpstream"), type="logical", help="Ignore upstream"),
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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21 make_option(c("-k","--ignoreDownstream"), type="logical", help="Ignore downstream"),
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22 make_option(c("-f","--format"), type="character", help="Output format (interval or tabular)."),
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23 make_option(c("-p","--plots"), type="logical", help="PDF of plots."),
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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24 make_option(c("-r","--rdata"), type="logical", help="Output RData file.")
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25 )
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27 parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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28 args = parse_args(parser)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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30 peaks = args$infile
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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31 gtf = args$gtf
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32 up = args$upstream
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33 down = args$downstream
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34 format = args$format
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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35
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36 if (!is.null(args$flankgeneinfo)) {
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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37 flankgeneinfo <- TRUE
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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38 } else {
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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39 flankgeneinfo <- FALSE
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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40 }
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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41
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42 if (!is.null(args$ignoreUpstream)) {
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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43 ignoreUpstream <- TRUE
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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44 } else {
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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45 ignoreUpstream <- FALSE
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46 }
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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47
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48 if (!is.null(args$ignoreDownstream)) {
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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49 ignoreDownstream <- TRUE
3ff6333973aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit d83142dbe2432fcb0f56dcd6311a05c061628ecc
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50 } else {
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51 ignoreDownstream <- FALSE
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52 }
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53
1
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54 peaks <- readPeakFile(peaks)
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55
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56 # Make TxDb from GTF
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57 txdb <- makeTxDbFromGFF(gtf, format="gtf")
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58
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59 # Annotate peaks
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60 peakAnno <- annotatePeak(peaks, TxDb=txdb,
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61 tssRegion=c(-up, down),
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62 addFlankGeneInfo=flankgeneinfo,
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63 flankDistance=args$flankgenedist,
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64 ignoreUpstream=ignoreUpstream,
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65 ignoreDownstream=ignoreDownstream)
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66
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67 # Add gene name
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68 features <- import(gtf, format="gtf")
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69 ann <- unique(mcols(features)[, c("gene_id", "gene_name")])
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70 res <- as.data.frame(peakAnno)
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71 res <- merge(res, ann, by.x="geneId", by.y="gene_id")
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72 names(res)[names(res) == "gene_name"] <- "geneName"
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73
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74 #Extract metadata cols, 1st is geneId, rest should be from col 7 to end
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75 metacols <- res[, c(7:ncol(res), 1)]
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76 # Convert from 1-based to 0-based format
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77 if (format == "interval") {
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78 metacols <- apply(as.data.frame(metacols), 1, function(col) paste(col, collapse="|"))
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79 resout <- data.frame(res$seqnames,
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80 res$start - 1,
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81 res$end,
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82 metacols)
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83 colnames(resout)[1:4] <- c("Chrom", "Start", "End", "Comment")
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84 } else {
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85 resout <- data.frame(res$seqnames,
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86 res$start - 1,
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87 res$end,
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88 metacols)
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89 colnames(resout)[1:3] <- c("Chrom", "Start", "End")
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90 }
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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91 write.table(resout, file="out.tab", sep="\t", row.names=FALSE, quote=FALSE)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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92
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195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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93 if (!is.null(args$plots)) {
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2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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94 pdf("out.pdf", width=14)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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95 plotAnnoPie(peakAnno)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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96 plotAnnoBar(peakAnno)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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97 vennpie(peakAnno)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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98 upsetplot(peakAnno)
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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99 plotDistToTSS(peakAnno, title="Distribution of transcription factor-binding loci\nrelative to TSS")
2019b4dd86a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 3419a5a5e19a93369c8c20a39babe5636a309292
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100 dev.off()
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101 }
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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102
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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103 ## Output RData file
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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104
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105 if (!is.null(args$rdata)) {
195cba35110e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chipseeker commit 861db0d1f76bb320f49c2501f4e656cf88d389ce
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106 save.image(file = "ChIPseeker_analysis.RData")
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107 }