Mercurial > repos > galaxyp > psm_to_sam

annotate PSM2SAM.R @ 0:c506e5dac2bb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
author galaxyp
date Fri, 02 Oct 2015 14:14:15 -0400
parents
children 34f9e847dd4e
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c506e5dac2bb planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit b37186806a83fb3a59a1b4ccb1d44667d5224277-dirty
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1 #!/usr/bin/env Rscript
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3 ## begin warning handler
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4 withCallingHandlers({
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6 library(methods) # Because Rscript does not always do this
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8 options('useFancyQuotes' = FALSE)
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10 suppressPackageStartupMessages(library("optparse"))
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11 suppressPackageStartupMessages(library("RGalaxy"))
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14 option_list <- list()
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16 option_list$passedPSM <- make_option('--passedPSM', type='character')
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17 option_list$XScolumn <- make_option('--XScolumn', type='character')
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18 option_list$exon_anno <- make_option('--exon_anno', type='character')
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19 option_list$proteinseq <- make_option('--proteinseq', type='character')
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20 option_list$procodingseq <- make_option('--procodingseq', type='character')
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21 option_list$header <- make_option('--header', type='character')
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22 option_list$OutputFile <- make_option('--OutputFile', type='character')
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25 opt <- parse_args(OptionParser(option_list=option_list))
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30 PSMtab2SAM <- function(
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31 passedPSM_file = GalaxyInputFile(required=TRUE),
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32 exon_anno_file = GalaxyInputFile(),
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33 proteinseq_file = GalaxyInputFile(),
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34 procodingseq_file = GalaxyInputFile(),
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35 header_file = GalaxyInputFile(),
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36 XScolumn = GalaxyCharacterParam(required=TRUE),
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37 OutputFile = GalaxyOutput("proSAM","sam"))
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38 {
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39 if (length(exon_anno_file) == 0) { exon_anno_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/exon_anno.RData" }
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40 if (length(proteinseq_file) == 0) { proteinseq_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/proseq.RData" }
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41 if (length(procodingseq_file) == 0) { procodingseq_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/procodingseq.RData" }
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42 if (length(header_file) == 0) { header_file = "/export/src/tools-galaxyp-chambm/tools/bumbershoot/psm_to_sam/tool-data/header_refseq_hg19.txt" }
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43
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44 if (!file.exists(header_file)) { gstop("failed to read header file") }
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45 if (file.exists(OutputFile))
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46 {
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47 if (file.info(OutputFile)$size > 0) { gstop("output file already exists") }
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48 else
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49 {
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50 tryCatch(
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51 {
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52 file.remove(OutputFile)
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53 }, error=function(err)
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54 {
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55 gstop("failed to read empty existing file")
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56 })
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57 }
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58 }
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59
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60 suppressPackageStartupMessages(library(GenomicRanges))
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61 suppressPackageStartupMessages(library(Biostrings))
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62
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63 options(stringsAsFactors=FALSE)
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64
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65 scoreName = XScolumn
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66 columnName = gsub(":", "_", scoreName)
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67
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68 passedPSM <- tryCatch({
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69 #read.delim(passedPSM_file, row.names=1)
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70 suppressPackageStartupMessages(library(RSQLite))
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71 drv <- dbDriver("SQLite")
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72 con <- dbConnect(drv, passedPSM_file)
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73
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74 # do case-insensitive search for the score name
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75 res <- dbSendQuery(con, paste("SELECT Id, Name FROM PeptideSpectrumMatchScoreName WHERE lower(Name)=lower('", scoreName, "')", sep=""))
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76 scoreInfo = fetch(res, n=1)
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77 scoreId = scoreInfo["Id"]
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78 realScoreName = scoreInfo["Name"] # original case
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79 dbClearResult(res)
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80
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81 sql <- paste("SELECT ss.Name as SourceName, s.NativeID",
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82 ", psm.ObservedNeutralMass AS precursor_neutral_mass",
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83 ", psm.Charge AS assumed_charge",
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84 ", s.ScanTimeInSeconds AS retention_time_sec",
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85 ", psm.Rank AS hit_rank",
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86 ", IFNULL(SUBSTR(pd.Sequence, pi.Offset+1, pi.Length), pep.DecoySequence) AS peptide",
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87 ", pro.Accession AS protein",
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88 ", COUNT(DISTINCT pro.Id) AS num_tot_proteins",
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89 ", psm.ObservedNeutralMass - (psm.MonoisotopicMassError - ROUND(psm.MonoisotopicMassError) * 1.0026) AS calc_neutral_pep_mass",
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90 ", psm.MonoisotopicMassError - ROUND(psm.MonoisotopicMassError) * 1.0026 AS massdiff",
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91 ", CTerminusIsSpecific+NTerminusIsSpecific AS num_tol_term",
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92 ", MissedCleavages AS num_missed_cleavages",
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93 ", psm.QValue AS qvalue",
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94 ", psmScore.Value AS ", columnName,
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95 ", GROUP_CONCAT(DISTINCT pm.Offset || ';' || mod.MonoMassDelta) AS modification",
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96 "FROM PeptideSpectrumMatch psm",
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97 "JOIN Spectrum s ON psm.Spectrum=s.Id",
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98 "JOIN SpectrumSource ss ON s.Source=ss.Id",
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99 "JOIN PeptideInstance pi ON psm.Peptide=pi.Peptide",
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100 "JOIN Protein pro ON pi.Protein=pro.Id",
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101 "JOIN Peptide pep ON pi.Peptide=pep.Id",
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102 "JOIN PeptideSpectrumMatchScore psmScore ON psmScore.PsmId=psm.Id AND ScoreNameId=", scoreId,
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103 "LEFT JOIN ProteinData pd ON pro.Id=pd.Id",
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104 "LEFT JOIN PeptideModification pm ON psm.Id=pm.PeptideSpectrumMatch",
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105 "LEFT JOIN Modification mod ON pm.Modification=mod.Id",
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106 "GROUP BY psm.Id"
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107 )
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108
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109 res <- dbSendQuery(con, sql)
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110 passedPSM <- fetch(res, n=-1)
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111 dbClearResult(res)
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112 dbDisconnect(con)
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113 passedPSM
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114 }, error=function(err) {
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115 gstop("failed to read passedPSM: ", err)
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116 })
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117
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118 tryCatch({
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119 load(exon_anno_file)
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120 exon_anno <- exon
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121 }, error=function(err) {
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122 gstop("failed to read exon_anno: ", conditionMessage(err))
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123 })
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124
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125 tryCatch({
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126 load(proteinseq_file)
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127 }, error=function(err) {
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128 gstop("failed to read proteinseq: ", conditionMessage(err))
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129 })
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130
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131 tryCatch({
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132 load(procodingseq_file)
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133 }, error=function(err) {
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134 gstop("failed to read procodingseq: ", conditionMessage(err))
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135 })
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136
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137 PEP <- passedPSM[, 'peptide']
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138 #Spectrumid <- paste(passedPSM[, 'SourceName'], gsub(" ", "_", passedPSM[, 'NativeID']), sep="/")
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139 Spectrumid <- paste(passedPSM[, 'SourceName'], passedPSM[, 'NativeID'], sep="/")
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140 #PEP_SEQ <- formatPep(spectra[, 'Sequence'])
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141
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142 SAM <- c()
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143
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144 spectrumcount <- table(Spectrumid)
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145
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146 for(i in 1:dim(passedPSM)[1]){
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147 #print(i)
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148 peptide <- PEP[i]
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149 QNAME <- Spectrumid[i]
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150 idx <- grep(peptide, proteinseq[, 'peptide'], fixed=TRUE)
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151 if(length(idx) == 0){
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152 RNAME <- '*'
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153 MAPQ <- 255
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154 RNEXT <- '*'
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155 PNEXT <- 0
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156 TLEN <- 0
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157 QUAL <- '*'
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158 POS <- 0
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159 SEQ <- '*'
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160 CIGAR <- '*'
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161 FLAG <- 0x4
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162 annoted <- '?'
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163 XA <- paste('XA:Z:', annoted, sep='')
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164 res <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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165 as.character(SEQ), QUAL, XA)
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166 res <- unique(data.frame(t(res)))
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167 }else{
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168 pro <- proteinseq[idx, ]
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169 sta_pos <- unlist(lapply(pro[, 'peptide'], function(x)
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170 regexpr(peptide, x, fixed=TRUE)))
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171 pep_len <- nchar(peptide)
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172 end_pos <- sta_pos + pep_len - 1
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173
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174 coding <- procodingseq[match(pro[, 'pro_name'],
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175 procodingseq[, 'pro_name']), ]
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176 code_s <- (sta_pos-1) * 3 + 1
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177 code_e <- end_pos * 3
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178 codingseq <- substring(coding[, 'coding'], code_s, code_e)
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179
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180
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181
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182 exonp <- lapply(pro[, 'tx_name'], function(x)
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183 exon_anno[exon_anno[, 'tx_name']==x, ])
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184
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185 exonp <- lapply(exonp, function(x){
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186 if(length(unique(x[, 'tx_id'])) > 1){
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187 x[grep(x[1, 'tx_id'], x[, 'tx_id'],
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188 fixed=TRUE), ]
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189 }else x
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190 })
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191
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192 if(passedPSM[i, 'hit_rank'] == 1) pri <- TRUE else pri <- FALSE
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193
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194 res <- mapply(function(x, y, z, m)
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195 if(dim(z)[1] == 0){
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196 .proteinUnannotated(x, y, z, m, primary=pri)
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197 }else{
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198 if((nchar(m) != 3*pep_len) | (y > max(z[, 'cds_end'],
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199 na.rm = TRUE))){
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200 #if(toString(translate(DNAString(m))) != peptide){
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201 .peptideUnannotated(x, y, z, m, primary=pri)
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202 }else{
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203 .MapCoding2genome(x, y, z, m, primary=pri)
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204 }
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205 },
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206 code_s, code_e, exonp, codingseq)
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207
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208 res <- unique(data.frame(t(res)))
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209
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210 }
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211 XL <- paste('XL:i:', as.numeric(spectrumcount[QNAME]), sep='')
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212 NH <- paste('NH:i:', dim(res)[1], sep='')
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213 XP <- paste('XP:Z:', peptide, sep='')
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214 #XF <- paste('XF:f:', round(passedPSM[i, XFcolumn], digits=4), sep='')
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215 XC <- paste('XC:i:', passedPSM[i, 'assumed_charge'], sep='')
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216 XS <- paste('XS:f:', round(as.numeric(passedPSM[i, columnName]),
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217 digits=4), sep='')
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218 #XA <- paste('XA:Z:', annoted, sep='')
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219 XN <- paste('XN:i:', passedPSM[i, 'num_missed_cleavages'], sep='')
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220 XT <- paste('XT:i:', passedPSM[i, 'num_tol_term'], sep='')
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221
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222 XM <- ifelse(is.na(passedPSM[i, 'modification']), paste('XM:Z:-'),
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223 paste('XM:Z:', passedPSM[i, 'modification'], sep=''))
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224
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225 res <- cbind(QNAME, res, NH, XL, XP, XC, XS, XM, XN, XT)
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226 SAM <- rbind(SAM, res)
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227 }
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228
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229 file.copy(header_file, OutputFile)
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230 write.table(SAM, file=OutputFile, sep='\t', quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE)
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231 }
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232
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233
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234
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235 .proteinUnannotated <-function(c_sta, c_end, exon_anno, cseq, primary=TRUE, ...)
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236 {
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237 RNAME <- '*'
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238 MAPQ <- 255
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239 RNEXT <- '*'
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240 PNEXT <- 0
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241 TLEN <- 0
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242 QUAL <- '*'
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243 POS <- 0
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244 SEQ <- '*'
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245 CIGAR <- '*'
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246 annoted <- 2
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247 XA <- paste('XA:Z:', annoted, sep='')
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galaxyp
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248 FLAG <- 0x4
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249
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galaxyp
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250 tmp <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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251 as.character(SEQ), QUAL, XA)
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252 tmp
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253 }
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254
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255
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256
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257 .peptideUnannotated <- function(c_sta, c_end, exon_anno, cseq, primary=TRUE, ...)
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258 {
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galaxyp
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259 #RNAME <- as.character(exon_anno[1, 'chromosome_name'])
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260 RNAME <- '*'
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galaxyp
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261 MAPQ <- 255
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262 RNEXT <- '*'
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263 PNEXT <- 0
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264 TLEN <- 0
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265 QUAL <- '*'
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266 POS <- 0
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267 SEQ <- '*'
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268 CIGAR <- '*'
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galaxyp
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269 annoted <- 1
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270 XA <- paste('XA:Z:', annoted, sep='')
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271 FLAG <- 0x4
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272 #if(exon_anno[1, 'strand'] == '+'){
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273 # FLAG <- ifelse(primary==TRUE, 0x00, 0x00+0x100)
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parents:
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274 #}else{
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275 # FLAG <- ifelse(primary==TRUE, 0x10, 0x10+0x100)
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276 #}
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277
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278 tmp <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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279 as.character(SEQ), QUAL, XA)
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280 tmp
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281 }
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282
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283
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284
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galaxyp
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285 .MapCoding2genome <- function(c_sta, c_end, exon_anno, cseq, primary=TRUE, ...)
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286 {
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galaxyp
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287 idxs <- intersect(which(exon_anno[, 'cds_start'] <= c_sta),
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galaxyp
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288 which(exon_anno[, 'cds_end'] >= c_sta))
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galaxyp
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289 idxe <- intersect(which(exon_anno[, 'cds_start'] <= c_end),
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galaxyp
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290 which(exon_anno[, 'cds_end'] >= c_end))
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galaxyp
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291 len <- c_end - c_sta + 1
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galaxyp
parents:
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292 RNAME <- as.character(exon_anno[1, 'chromosome_name'])
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galaxyp
parents:
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293 MAPQ <- 255
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294 RNEXT <- '*'
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galaxyp
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295 PNEXT <- 0
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296 TLEN <- 0
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297 QUAL <- '*'
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galaxyp
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298 annoted <- 0
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galaxyp
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299 XA <- paste('XA:Z:', annoted, sep='')
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galaxyp
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300
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galaxyp
parents:
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301 if(exon_anno[1, 'strand'] == '+'){
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galaxyp
parents:
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302 POS <- exon_anno[idxs, 'cds_chr_start'] + c_sta -
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galaxyp
parents:
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303 exon_anno[idxs, 'cds_start']
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galaxyp
parents:
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304 SEQ <- DNAString(cseq)
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galaxyp
parents:
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305 FLAG <- ifelse(primary==TRUE, 0x00, 0x00+0x100)
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parents:
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306
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galaxyp
parents:
diff changeset
307 }else{
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galaxyp
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308 POS <- exon_anno[idxe, 'cds_chr_start'] +
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galaxyp
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309 exon_anno[idxe, 'cds_end'] - c_end
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galaxyp
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310 SEQ <- reverseComplement(DNAString(cseq))
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311 FLAG <- ifelse(primary==TRUE, 0x10, 0x10 + 0x100)
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312 }
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313
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parents:
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314 if(idxe == idxs){
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parents:
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315 CIGAR <- paste(len, 'M', sep='')
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galaxyp
parents:
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316 }else{
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317 if(exon_anno[1, 'strand'] == '+'){
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318 #insert <- exon_anno[idxe, 'cds_chr_start'] - exon_anno[idxs,
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319 # 'cds_chr_end']- 1
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320 part1 <- exon_anno[idxs, 'cds_end'] - c_sta + 1
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321 part2 <- c_end - exon_anno[idxe, 'cds_start'] + 1
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322
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galaxyp
parents:
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323 insert <- unlist(lapply(1:(idxe - idxs), function(x)
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324 paste(exon_anno[idxs + x, 'cds_chr_start'] -
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galaxyp
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325 exon_anno[idxs+x-1, 'cds_chr_end']- 1, 'N', sep='')))
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326 if(idxe-idxs >1){
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327 innerexon <- unlist(lapply(1:(idxe-idxs-1), function(x)
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328 paste(exon_anno[idxs + x, 'cds_chr_end'] -
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329 exon_anno[idxs + x, 'cds_chr_start'] + 1, 'M',
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330 sep='')))
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331 }else{ innerexon <- ''}
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332
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333 #ifelse(idxe-idxs >1, unlist(lapply(1:(idxe-idxs-1), function(x)
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334 #paste(exon_anno[idxs+x, 'cds_chr_end'] -
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335 # exon_anno[idxs+x, 'cds_chr_start']+1,
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336 # 'M', sep=''))), '')
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337 midpattern <- rep(NA, length(insert) + length(innerexon))
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338 midpattern[seq(1, length(insert) + length(innerexon),
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339 by=2)] <- insert
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340 midpattern[seq(2, length(insert) + length(innerexon),
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341 by=2)] <- innerexon
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342 midpattern <- paste(midpattern, collapse='')
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343
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344 }else{
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345 #insert <- exon_anno[idxs, 'cds_chr_start'] -
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346 # exon_anno[idxe, 'cds_chr_end']- 1
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347 part1 <- c_end- exon_anno[idxe, 'cds_start'] + 1
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348 part2 <- exon_anno[idxs, 'cds_end'] - c_sta + 1
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349
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350 insert <- unlist(lapply(1:(idxe-idxs), function(x)
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351 paste(exon_anno[idxe - x, 'cds_chr_start'] -
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352 exon_anno[idxe-x + 1, 'cds_chr_end']- 1,
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353 'N', sep='')))
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354 if(idxe-idxs >1){
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355 innerexon <- unlist(lapply(1:(idxe-idxs-1), function(x)
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356 paste(exon_anno[idxe-x, 'cds_chr_end'] -
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357 exon_anno[idxe-x, 'cds_chr_start']+1, 'M', sep='')))
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358 }else{ innerexon <-''}
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359
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360 midpattern <- rep(NA, length(insert)+length(innerexon))
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361 midpattern[seq(1, length(insert) + length(innerexon),
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362 by=2)] <- insert
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363 midpattern[seq(2, length(insert) + length(innerexon),
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364 by=2)] <- innerexon
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365 midpattern <- paste(midpattern, collapse='')
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366
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367 }
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368
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369 CIGAR <- paste(part1, 'M', midpattern, part2, 'M', sep='')
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370 }
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371
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372 tmp <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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373 as.character(SEQ), QUAL, XA)
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374 tmp
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375 }
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376
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377
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378 params <- list()
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379 for(param in names(opt))
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380 {
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381 if (!param == "help")
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382 params[param] <- opt[param]
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383 }
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384
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385 setClass("GalaxyRemoteError", contains="character")
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386 wrappedFunction <- function(f)
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387 {
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388 tryCatch(do.call(f, params),
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389 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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390 }
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391
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392
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393 suppressPackageStartupMessages(library(RGalaxy))
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394 do.call(PSMtab2SAM, params)
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395
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396 ## end warning handler
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397 }, warning = function(w) {
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398 cat(paste("Warning:", conditionMessage(w), "\n"))
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399 invokeRestart("muffleWarning")
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400 })