Mercurial > repos > galaxyp > psm_to_sam

annotate PSM2SAM.R @ 3:16c4cc7793e9 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit d4b5497065b853ed094aebc9e4185e9995c5e0e0
author galaxyp
date Wed, 01 Nov 2017 19:28:25 -0400
parents 757ecf27b4a9
children
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90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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1 #!/usr/bin/env Rscript
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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3 ## begin warning handler
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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4 withCallingHandlers({
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6 library(methods) # Because Rscript does not always do this
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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8 options('useFancyQuotes' = FALSE)
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10 suppressPackageStartupMessages(library("optparse"))
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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11 suppressPackageStartupMessages(library("RGalaxy"))
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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14 option_list <- list()
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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16 option_list$exon_anno <- make_option('--exon_anno', type='character')
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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17 option_list$proteinseq <- make_option('--proteinseq', type='character')
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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18 option_list$procodingseq <- make_option('--procodingseq', type='character')
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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19 option_list$bam_file <- make_option('--bam', type='character')
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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20 option_list$idpDB_file <- make_option('--idpDB', type='character')
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21 option_list$pepXmlTab_file <- make_option('--pepXmlTab', type='character')
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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22 option_list$peptideShakerPsmReport_file <- make_option('--peptideShakerPsmReport', type='character')
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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23 option_list$variantAnnotation_file <- make_option('--variantAnnotation', type='character')
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24 option_list$searchEngineScore <- make_option('--searchEngineScore', type='character')
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27 opt <- parse_args(OptionParser(option_list=option_list))
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30 psm2sam <- function(
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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31 exon_anno_file = GalaxyInputFile(required=TRUE),
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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32 proteinseq_file = GalaxyInputFile(required=TRUE),
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33 procodingseq_file = GalaxyInputFile(required=TRUE),
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34 bam_file = GalaxyInputFile(required=TRUE),
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35 idpDB_file = GalaxyInputFile(required=FALSE),
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36 pepXmlTab_file = GalaxyInputFile(required=FALSE),
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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37 peptideShakerPsmReport_file = GalaxyInputFile(required=FALSE),
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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38 variantAnnotation_file = GalaxyInputFile(required=FALSE),
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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39 searchEngineScore = GalaxyCharacterParam(required=FALSE)
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40 )
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41 {
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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42 options(stringsAsFactors = FALSE)
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44 if (length(bam_file) == 0)
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45 {
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46 stop("BAM file must be specified to provide sequence headers")
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47 }
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49 outputHeader = grep("^@(?!PG)", readLines(bam_file, n=500, warn=FALSE), value=TRUE, perl=TRUE)
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50 if (length(outputHeader) == 0)
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51 {
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52 stop("failed to read header lines from bam_file")
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53 }
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55 # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github)
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56 download.file("https://github.com/chambm/customProDB/archive/9db2223ef9932e50124b92d1bc49206af1f40fb3.zip", "customProDB.zip", quiet=TRUE)
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57 unzip("customProDB.zip")
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58 devtools::load_all("customProDB-9db2223ef9932e50124b92d1bc49206af1f40fb3")
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60 # load proBAMr from GitHub
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61 download.file("https://github.com/chambm/proBAMr/archive/a03edf68f51215be40717c5374f39ce67bd2e68b.zip", "proBAMr.zip", quiet=TRUE)
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62 unzip("proBAMr.zip")
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63 devtools::load_all("proBAMr-a03edf68f51215be40717c5374f39ce67bd2e68b")
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65 psmInputLength = length(idpDB_file)+length(pepXmlTab_file)+length(peptideShakerPsmReport_file)
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66 if (psmInputLength == 0)
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67 {
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68 stop("one of the input PSM file parameters must be specified")
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69 }
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70 else if (psmInputLength > 1)
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71 {
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72 stop("only one of the input PSM file parameters can be specified")
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73 }
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75 if (length(idpDB_file) > 0)
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76 {
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77 if (length(searchEngineScore) == 0)
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78 stop("searchEngineScore parameter must be specified when reading IDPicker PSMs, e.g. 'MyriMatch:MVH'")
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79 passedPSM = readIdpDB(idpDB_file, searchEngineScore)
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80 }
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81 else if (length(pepXmlTab_file) > 0)
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82 {
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83 if (length(searchEngineScore) == 0)
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84 stop("searchEngineScore parameter must be specified when reading pepXmlTab PSMs, e.g. 'mvh'")
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85 passedPSM = readPepXmlTab(pepXmlTab_file, searchEngineScore)
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86 }
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87 else if (length(peptideShakerPsmReport_file) > 0)
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88 {
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89 if (length(searchEngineScore) > 0)
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90 warning("searchEngineScore parameter is ignored when reading PeptideShaker PSM report")
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91 passedPSM = readPeptideShakerPsmReport(peptideShakerPsmReport_file)
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92 }
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93
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94 load(exon_anno_file)
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95 load(proteinseq_file)
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96 load(procodingseq_file)
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97
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98 if (length(variantAnnotation_file) > 0)
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99 {
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
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100 load(variantAnnotation_file) # variantAnnotation list, with members snvprocoding/snvproseq and indelprocoding/indelproseq
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101
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102 varprocoding = unique(rbind(variantAnnotation$snvprocoding, variantAnnotation$indelprocoding))
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103 varproseq = unique(rbind(variantAnnotation$snvproseq, variantAnnotation$indelproseq))
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104 }
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105 else
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106 {
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107 varprocoding = NULL
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108 varproseq = NULL
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109 }
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110
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111 # add proBAMr program key
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112 outputHeader = c(outputHeader, paste0("@PG\tID:proBAMr\tVN:", packageVersion("proBAMr")))
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113
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114 # first write header lines to the output SAM
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115 writeLines(outputHeader, "output.sam")
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116
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117 # then write the PSM "reads"
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118 PSMtab2SAM(passedPSM, exon,
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119 proteinseq, procodingseq,
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120 varproseq, varprocoding,
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121 outfile = "output.sam",
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122 show_progress = FALSE)
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123
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124 invisible(NULL)
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125 }
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126
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127 params <- list()
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128 for(param in names(opt))
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129 {
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130 if (!param == "help")
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131 params[param] <- opt[param]
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132 }
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133
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134 setClass("GalaxyRemoteError", contains="character")
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135 wrappedFunction <- function(f)
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136 {
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137 tryCatch(do.call(f, params),
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138 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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139 }
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140
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141
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142 suppressPackageStartupMessages(library(RGalaxy))
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143 do.call(psm2sam, params)
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144
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145 ## end warning handler
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146 }, warning = function(w) {
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147 cat(paste("Warning:", conditionMessage(w), "\n"))
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148 invokeRestart("muffleWarning")
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149 })