Mercurial > repos > galaxyp > psm_to_sam

annotate PSM2SAM.R @ 3:ce09f1a1bbad draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm_to_sam commit 141369f97aa2804d2bbfd9ed620ea2a5574994c2-dirty
author galaxyp
date Thu, 28 Jan 2016 18:40:54 -0500
parents 34f9e847dd4e
children cd69250e1150
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1 #!/usr/bin/env Rscript
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3 initial.options <- commandArgs(trailingOnly = FALSE)
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4 script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
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6 ## begin warning handler
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7 withCallingHandlers({
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9 library(methods) # Because Rscript does not always do this
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11 options('useFancyQuotes' = FALSE)
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13 suppressPackageStartupMessages(library("optparse"))
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14 suppressPackageStartupMessages(library("RGalaxy"))
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17 option_list <- list()
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19 option_list$passedPSM <- make_option('--passedPSM', type='character')
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20 option_list$XScolumn <- make_option('--XScolumn', type='character')
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21 option_list$exon_anno <- make_option('--exon_anno', type='character')
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22 option_list$proteinseq <- make_option('--proteinseq', type='character')
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23 option_list$procodingseq <- make_option('--procodingseq', type='character')
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24 option_list$header <- make_option('--header', type='character')
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25 option_list$OutputFile <- make_option('--OutputFile', type='character')
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28 opt <- parse_args(OptionParser(option_list=option_list))
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33 PSMtab2SAM <- function(
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34 passedPSM_file = GalaxyInputFile(required=TRUE),
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35 exon_anno_file = GalaxyInputFile(required=TRUE),
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36 proteinseq_file = GalaxyInputFile(required=TRUE),
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37 procodingseq_file = GalaxyInputFile(required=TRUE),
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38 header_file = GalaxyInputFile(required=TRUE),
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39 XScolumn = GalaxyCharacterParam(required=TRUE),
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40 OutputFile = GalaxyOutput("proSAM","sam"))
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41 {
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42 if (!file.exists(header_file)) { gstop("failed to read header file") }
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43 if (file.exists(OutputFile))
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44 {
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45 if (file.info(OutputFile)$size > 0) { gstop("output file already exists") }
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46 else
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47 {
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48 tryCatch(
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49 {
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50 file.remove(OutputFile)
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51 }, error=function(err)
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52 {
3
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53 gstop("failed to remove empty existing file")
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54 })
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55 }
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56 }
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57
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58 suppressPackageStartupMessages(library(GenomicRanges))
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59 suppressPackageStartupMessages(library(Biostrings))
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61 options(stringsAsFactors=FALSE)
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62
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63 scoreName = XScolumn
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64 columnName = gsub("[^A-Z0-9]", "_", scoreName)
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65
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66 passedPSM <- tryCatch({
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67 #read.delim(passedPSM_file, row.names=1)
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68 suppressPackageStartupMessages(library(RSQLite))
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69 drv <- dbDriver("SQLite")
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70 con <- dbConnect(drv, passedPSM_file)
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71
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72 # do case-insensitive search for the score name
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73 res <- dbSendQuery(con, paste("SELECT Id, Name FROM PeptideSpectrumMatchScoreName WHERE lower(Name)=lower('", scoreName, "')", sep=""))
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74 scoreInfo = fetch(res, n=1)
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75 scoreId = scoreInfo["Id"]
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76 realScoreName = scoreInfo["Name"] # original case
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77 dbClearResult(res)
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78
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79 sql <- paste("SELECT ss.Name as SourceName, s.NativeID",
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80 ", psm.ObservedNeutralMass AS precursor_neutral_mass",
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81 ", psm.Charge AS assumed_charge",
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82 ", s.ScanTimeInSeconds AS retention_time_sec",
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83 ", psm.Rank AS hit_rank",
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84 ", IFNULL(SUBSTR(pd.Sequence, pi.Offset+1, pi.Length), pep.DecoySequence) AS peptide",
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85 ", pro.Accession AS protein",
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86 ", COUNT(DISTINCT pro.Id) AS num_tot_proteins",
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87 ", psm.ObservedNeutralMass - (psm.MonoisotopicMassError - ROUND(psm.MonoisotopicMassError) * 1.0026) AS calc_neutral_pep_mass",
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88 ", psm.MonoisotopicMassError - ROUND(psm.MonoisotopicMassError) * 1.0026 AS massdiff",
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89 ", CTerminusIsSpecific+NTerminusIsSpecific AS num_tol_term",
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90 ", MissedCleavages AS num_missed_cleavages",
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91 ", psm.QValue AS qvalue",
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92 ", psmScore.Value AS ", columnName,
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93 ", GROUP_CONCAT(DISTINCT pm.Offset || ';' || mod.MonoMassDelta) AS modification",
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94 "FROM PeptideSpectrumMatch psm",
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95 "JOIN Spectrum s ON psm.Spectrum=s.Id",
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96 "JOIN SpectrumSource ss ON s.Source=ss.Id",
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97 "JOIN PeptideInstance pi ON psm.Peptide=pi.Peptide",
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98 "JOIN Protein pro ON pi.Protein=pro.Id",
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99 "JOIN Peptide pep ON pi.Peptide=pep.Id",
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100 "JOIN PeptideSpectrumMatchScore psmScore ON psmScore.PsmId=psm.Id AND ScoreNameId=", scoreId,
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101 "LEFT JOIN ProteinData pd ON pro.Id=pd.Id",
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102 "LEFT JOIN PeptideModification pm ON psm.Id=pm.PeptideSpectrumMatch",
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103 "LEFT JOIN Modification mod ON pm.Modification=mod.Id",
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104 "GROUP BY psm.Id"
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105 )
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106
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107 res <- dbSendQuery(con, sql)
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108 passedPSM <- fetch(res, n=-1)
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109 dbClearResult(res)
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110 dbDisconnect(con)
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111 passedPSM
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112 }, error=function(err) {
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113 gstop("failed to read passedPSM: ", err)
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114 })
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115
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116 tryCatch({
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117 load(exon_anno_file)
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118 exon_anno <- exon
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119 }, error=function(err) {
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120 gstop("failed to read exon_anno: ", conditionMessage(err))
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121 })
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122
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123 tryCatch({
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124 load(proteinseq_file)
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125 }, error=function(err) {
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126 gstop("failed to read proteinseq: ", conditionMessage(err))
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127 })
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128
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129 tryCatch({
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130 load(procodingseq_file)
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131 }, error=function(err) {
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132 gstop("failed to read procodingseq: ", conditionMessage(err))
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133 })
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134
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135 PEP <- passedPSM[, 'peptide']
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136 #Spectrumid <- paste(passedPSM[, 'SourceName'], gsub(" ", "_", passedPSM[, 'NativeID']), sep="/")
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137 Spectrumid <- paste(passedPSM[, 'SourceName'], passedPSM[, 'NativeID'], sep="/")
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138 #PEP_SEQ <- formatPep(spectra[, 'Sequence'])
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139
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140 SAM <- c()
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141
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142 spectrumcount <- table(Spectrumid)
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143
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144 for(i in 1:dim(passedPSM)[1]){
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145 #print(i)
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146 peptide <- PEP[i]
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147 QNAME <- Spectrumid[i]
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148 idx <- grep(peptide, proteinseq[, 'peptide'], fixed=TRUE)
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149 if(length(idx) == 0){
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150 RNAME <- '*'
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151 MAPQ <- 255
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152 RNEXT <- '*'
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153 PNEXT <- 0
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154 TLEN <- 0
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155 QUAL <- '*'
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156 POS <- 0
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157 SEQ <- '*'
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158 CIGAR <- '*'
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159 FLAG <- 0x4
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160 annoted <- '?'
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161 XA <- paste('XA:Z:', annoted, sep='')
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162 res <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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163 as.character(SEQ), QUAL, XA)
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164 res <- unique(data.frame(t(res)))
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165 }else{
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166 pro <- proteinseq[idx, ]
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167 sta_pos <- unlist(lapply(pro[, 'peptide'], function(x)
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168 regexpr(peptide, x, fixed=TRUE)))
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169 pep_len <- nchar(peptide)
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170 end_pos <- sta_pos + pep_len - 1
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171
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172 coding <- procodingseq[match(pro[, 'pro_name'],
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173 procodingseq[, 'pro_name']), ]
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174 code_s <- (sta_pos-1) * 3 + 1
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175 code_e <- end_pos * 3
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176 codingseq <- substring(coding[, 'coding'], code_s, code_e)
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177
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178
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179
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180 exonp <- lapply(pro[, 'tx_name'], function(x)
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181 exon_anno[exon_anno[, 'tx_name']==x, ])
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182
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183 exonp <- lapply(exonp, function(x){
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184 if(length(unique(x[, 'tx_id'])) > 1){
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185 x[grep(x[1, 'tx_id'], x[, 'tx_id'],
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186 fixed=TRUE), ]
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187 }else x
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188 })
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189
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190 if(passedPSM[i, 'hit_rank'] == 1) pri <- TRUE else pri <- FALSE
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191
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192 res <- mapply(function(x, y, z, m)
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193 if(dim(z)[1] == 0){
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194 .proteinUnannotated(x, y, z, m, primary=pri)
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195 }else{
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196 if((nchar(m) != 3*pep_len) | (y > max(z[, 'cds_end'],
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197 na.rm = TRUE))){
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198 #if(toString(translate(DNAString(m))) != peptide){
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199 .peptideUnannotated(x, y, z, m, primary=pri)
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200 }else{
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201 .MapCoding2genome(x, y, z, m, primary=pri)
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202 }
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203 },
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204 code_s, code_e, exonp, codingseq)
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205
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206 res <- unique(data.frame(t(res)))
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207
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208 }
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209 XL <- paste('XL:i:', as.numeric(spectrumcount[QNAME]), sep='')
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210 NH <- paste('NH:i:', dim(res)[1], sep='')
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211 XP <- paste('XP:Z:', peptide, sep='')
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212 #XF <- paste('XF:f:', round(passedPSM[i, XFcolumn], digits=4), sep='')
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213 XC <- paste('XC:i:', passedPSM[i, 'assumed_charge'], sep='')
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214 XS <- paste('XS:f:', round(as.numeric(passedPSM[i, columnName]),
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215 digits=4), sep='')
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216 #XA <- paste('XA:Z:', annoted, sep='')
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217 XN <- paste('XN:i:', passedPSM[i, 'num_missed_cleavages'], sep='')
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218 XT <- paste('XT:i:', passedPSM[i, 'num_tol_term'], sep='')
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219
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220 XM <- ifelse(is.na(passedPSM[i, 'modification']), paste('XM:Z:-'),
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221 paste('XM:Z:', passedPSM[i, 'modification'], sep=''))
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222
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223 res <- cbind(QNAME, res, NH, XL, XP, XC, XS, XM, XN, XT)
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224 SAM <- rbind(SAM, res)
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225 }
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226
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227 file.copy(header_file, OutputFile)
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228 write.table(SAM, file=OutputFile, sep='\t', quote=FALSE, row.names=FALSE, col.names=FALSE, append=TRUE)
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229 }
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230
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231
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232
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233 .proteinUnannotated <-function(c_sta, c_end, exon_anno, cseq, primary=TRUE, ...)
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234 {
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235 RNAME <- '*'
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236 MAPQ <- 255
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237 RNEXT <- '*'
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238 PNEXT <- 0
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239 TLEN <- 0
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240 QUAL <- '*'
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241 POS <- 0
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242 SEQ <- '*'
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243 CIGAR <- '*'
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244 annoted <- 2
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245 XA <- paste('XA:Z:', annoted, sep='')
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246 FLAG <- 0x4
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247
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galaxyp
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248 tmp <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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249 as.character(SEQ), QUAL, XA)
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250 tmp
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251 }
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252
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253
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254
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galaxyp
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255 .peptideUnannotated <- function(c_sta, c_end, exon_anno, cseq, primary=TRUE, ...)
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256 {
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257 #RNAME <- as.character(exon_anno[1, 'chromosome_name'])
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258 RNAME <- '*'
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galaxyp
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259 MAPQ <- 255
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260 RNEXT <- '*'
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261 PNEXT <- 0
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262 TLEN <- 0
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263 QUAL <- '*'
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264 POS <- 0
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265 SEQ <- '*'
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266 CIGAR <- '*'
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267 annoted <- 1
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268 XA <- paste('XA:Z:', annoted, sep='')
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269 FLAG <- 0x4
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270 #if(exon_anno[1, 'strand'] == '+'){
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271 # FLAG <- ifelse(primary==TRUE, 0x00, 0x00+0x100)
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parents:
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272 #}else{
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273 # FLAG <- ifelse(primary==TRUE, 0x10, 0x10+0x100)
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274 #}
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275
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276 tmp <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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277 as.character(SEQ), QUAL, XA)
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278 tmp
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279 }
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280
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281
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282
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283 .MapCoding2genome <- function(c_sta, c_end, exon_anno, cseq, primary=TRUE, ...)
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284 {
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galaxyp
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285 idxs <- intersect(which(exon_anno[, 'cds_start'] <= c_sta),
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galaxyp
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286 which(exon_anno[, 'cds_end'] >= c_sta))
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287 idxe <- intersect(which(exon_anno[, 'cds_start'] <= c_end),
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galaxyp
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288 which(exon_anno[, 'cds_end'] >= c_end))
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galaxyp
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289 len <- c_end - c_sta + 1
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galaxyp
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290 RNAME <- as.character(exon_anno[1, 'chromosome_name'])
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291 MAPQ <- 255
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galaxyp
parents:
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292 RNEXT <- '*'
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galaxyp
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293 PNEXT <- 0
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galaxyp
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294 TLEN <- 0
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295 QUAL <- '*'
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galaxyp
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296 annoted <- 0
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galaxyp
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297 XA <- paste('XA:Z:', annoted, sep='')
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298
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galaxyp
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299 if(exon_anno[1, 'strand'] == '+'){
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galaxyp
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300 POS <- exon_anno[idxs, 'cds_chr_start'] + c_sta -
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galaxyp
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301 exon_anno[idxs, 'cds_start']
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galaxyp
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302 SEQ <- DNAString(cseq)
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galaxyp
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303 FLAG <- ifelse(primary==TRUE, 0x00, 0x00+0x100)
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galaxyp
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304
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galaxyp
parents:
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305 }else{
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galaxyp
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306 POS <- exon_anno[idxe, 'cds_chr_start'] +
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galaxyp
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307 exon_anno[idxe, 'cds_end'] - c_end
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galaxyp
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308 SEQ <- reverseComplement(DNAString(cseq))
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galaxyp
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309 FLAG <- ifelse(primary==TRUE, 0x10, 0x10 + 0x100)
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310 }
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galaxyp
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311
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galaxyp
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312 if(idxe == idxs){
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313 CIGAR <- paste(len, 'M', sep='')
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galaxyp
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314 }else{
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galaxyp
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315 if(exon_anno[1, 'strand'] == '+'){
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316 #insert <- exon_anno[idxe, 'cds_chr_start'] - exon_anno[idxs,
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317 # 'cds_chr_end']- 1
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318 part1 <- exon_anno[idxs, 'cds_end'] - c_sta + 1
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319 part2 <- c_end - exon_anno[idxe, 'cds_start'] + 1
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320
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galaxyp
parents:
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321 insert <- unlist(lapply(1:(idxe - idxs), function(x)
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galaxyp
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322 paste(exon_anno[idxs + x, 'cds_chr_start'] -
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galaxyp
parents:
diff changeset
323 exon_anno[idxs+x-1, 'cds_chr_end']- 1, 'N', sep='')))
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324 if(idxe-idxs >1){
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galaxyp
parents:
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325 innerexon <- unlist(lapply(1:(idxe-idxs-1), function(x)
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326 paste(exon_anno[idxs + x, 'cds_chr_end'] -
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327 exon_anno[idxs + x, 'cds_chr_start'] + 1, 'M',
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328 sep='')))
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329 }else{ innerexon <- ''}
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330
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331 #ifelse(idxe-idxs >1, unlist(lapply(1:(idxe-idxs-1), function(x)
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332 #paste(exon_anno[idxs+x, 'cds_chr_end'] -
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333 # exon_anno[idxs+x, 'cds_chr_start']+1,
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334 # 'M', sep=''))), '')
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335 midpattern <- rep(NA, length(insert) + length(innerexon))
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336 midpattern[seq(1, length(insert) + length(innerexon),
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337 by=2)] <- insert
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338 midpattern[seq(2, length(insert) + length(innerexon),
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339 by=2)] <- innerexon
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340 midpattern <- paste(midpattern, collapse='')
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341
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342 }else{
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343 #insert <- exon_anno[idxs, 'cds_chr_start'] -
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344 # exon_anno[idxe, 'cds_chr_end']- 1
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345 part1 <- c_end- exon_anno[idxe, 'cds_start'] + 1
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346 part2 <- exon_anno[idxs, 'cds_end'] - c_sta + 1
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347
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348 insert <- unlist(lapply(1:(idxe-idxs), function(x)
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349 paste(exon_anno[idxe - x, 'cds_chr_start'] -
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350 exon_anno[idxe-x + 1, 'cds_chr_end']- 1,
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351 'N', sep='')))
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352 if(idxe-idxs >1){
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353 innerexon <- unlist(lapply(1:(idxe-idxs-1), function(x)
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354 paste(exon_anno[idxe-x, 'cds_chr_end'] -
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355 exon_anno[idxe-x, 'cds_chr_start']+1, 'M', sep='')))
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356 }else{ innerexon <-''}
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357
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358 midpattern <- rep(NA, length(insert)+length(innerexon))
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359 midpattern[seq(1, length(insert) + length(innerexon),
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360 by=2)] <- insert
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361 midpattern[seq(2, length(insert) + length(innerexon),
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362 by=2)] <- innerexon
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363 midpattern <- paste(midpattern, collapse='')
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364
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365 }
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366
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367 CIGAR <- paste(part1, 'M', midpattern, part2, 'M', sep='')
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368 }
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369
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370 tmp <- c(FLAG, RNAME, POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN,
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371 as.character(SEQ), QUAL, XA)
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372 tmp
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373 }
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374
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375
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376 params <- list()
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377 for(param in names(opt))
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378 {
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379 if (!param == "help")
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380 params[param] <- opt[param]
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381 }
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382
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383 setClass("GalaxyRemoteError", contains="character")
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384 wrappedFunction <- function(f)
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385 {
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386 tryCatch(do.call(f, params),
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387 error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
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388 }
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389
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390
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391 suppressPackageStartupMessages(library(RGalaxy))
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392 do.call(PSMtab2SAM, params)
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393
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394 ## end warning handler
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395 }, warning = function(w) {
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396 cat(paste("Warning:", conditionMessage(w), "\n"))
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397 invokeRestart("muffleWarning")
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398 })