R/fillMqparTemplate.R

In mariodejung/samplesubmission: Sample Submission User Web Interface

#' fills a template mqpar string with the given infos 
#' @param paramterGroups list of parameterGroups settings (mode, enzymes)
#' @param fastaFiles vector of fasta files paths
#' @param rawFiles optionaly vector of raw files paths
#' @param templateFile template File path. If NULL(standard), attempts read template from package by means of version
#' @param fixedFolder should MaxQuant create an extra folder.
#' @param MaxQuant version. for each version there should be a template file in the package 
#' @export
#' @return filled mqpar string
#' @examples
#' \dontrun{
#' fillMqparTemplate( list(list(mode=0, enzyme=c('LysC','GluC'))), c("human.fasta", "yeast.fasta"))
#' }

fillMqparTemplate <- function (parameterGroups,
                               fastaFiles,
                               rawFiles=NULL,
                               templateFile=NULL,
                               fixedFolder='',
                               version="1.5.2.8"){
  
  if(is.null(templateFile)){
    templateFile <- system.file('samplesubmission',
                                paste("mqpar.tmp.", version, ".xml", sep=""),
                                package='samplesubmission')
  }
  if(!file.exists(templateFile)){
    stop("cannot find template file: \n")
  }
  template <- readLines(templateFile)
  
  parameterGroup_string <- list()
  parameterGroup_string['1.6.3.4'] <- 
    "<parameterGroup>
  <msInstrument>0</msInstrument>
  <maxCharge>7</maxCharge>
  <minPeakLen>2</minPeakLen>
  <useMs1Centroids>False</useMs1Centroids>
  <useMs2Centroids>False</useMs2Centroids>
  <cutPeaks>True</cutPeaks>
  <gapScans>1</gapScans>
  <minTime>NaN</minTime>
  <maxTime>NaN</maxTime>
  <matchType>MatchFromAndTo</matchType>
  <intensityDetermination>0</intensityDetermination>
  <centroidMatchTol>8</centroidMatchTol>
  <centroidMatchTolInPpm>True</centroidMatchTolInPpm>
  <centroidHalfWidth>35</centroidHalfWidth>
  <centroidHalfWidthInPpm>True</centroidHalfWidthInPpm>
  <valleyFactor>1.4</valleyFactor>
  <isotopeValleyFactor>1.2</isotopeValleyFactor>
  <advancedPeakSplitting>False</advancedPeakSplitting>
  <intensityThreshold>0</intensityThreshold>
  <labelMods>
  <string></string>
  </labelMods>
  <lcmsRunType>Standard</lcmsRunType>
  <reQuantify>False</reQuantify>
  <lfqMode>0</lfqMode>
  <lfqSkipNorm>False</lfqSkipNorm>
  <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
  <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
  <lfqMaxFeatures>100000</lfqMaxFeatures>
  <neucodeMaxPpm>0</neucodeMaxPpm>
  <neucodeResolution>0</neucodeResolution>
  <neucodeResolutionInMda>False</neucodeResolutionInMda>
  <neucodeInSilicoLowRes>False</neucodeInSilicoLowRes>
  <fastLfq>True</fastLfq>
  <lfqRestrictFeatures>False</lfqRestrictFeatures>
  <lfqMinRatioCount>2</lfqMinRatioCount>
  <maxLabeledAa>0</maxLabeledAa>
  <maxNmods>5</maxNmods>
  <maxMissedCleavages>0</maxMissedCleavages>
  <multiplicity>1</multiplicity>
  <enzymeMode>%s</enzymeMode>
  <complementaryReporterType>0</complementaryReporterType>
  <reporterNormalization>0</reporterNormalization>
  <neucodeIntensityMode>0</neucodeIntensityMode>
  <fixedModifications>
  <string>Carbamidomethyl (C)</string>
  </fixedModifications>
  <enzymes>%s
  </enzymes>
  <enzymesFirstSearch>
  </enzymesFirstSearch>
  <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
  <useEnzymeFirstSearch>False</useEnzymeFirstSearch>
  <useVariableModificationsFirstSearch>False</useVariableModificationsFirstSearch>
  <variableModifications>
  <string>Oxidation (M)</string>
  <string>Acetyl (Protein N-term)</string>
  </variableModifications>
  <useMultiModification>False</useMultiModification>
  <multiModifications>
  </multiModifications>
  <isobaricLabels>
  </isobaricLabels>
  <neucodeLabels>
  </neucodeLabels>
  <variableModificationsFirstSearch>
  </variableModificationsFirstSearch>
  <hasAdditionalVariableModifications>False</hasAdditionalVariableModifications>
  <additionalVariableModifications>
  </additionalVariableModifications>
  <additionalVariableModificationProteins>
  </additionalVariableModificationProteins>
  <doMassFiltering>True</doMassFiltering>
  <firstSearchTol>20</firstSearchTol>
  <mainSearchTol>4.5</mainSearchTol>
  <searchTolInPpm>True</searchTolInPpm>
  <isotopeMatchTol>2</isotopeMatchTol>
  <isotopeMatchTolInPpm>True</isotopeMatchTolInPpm>
  <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
  <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
  <checkMassDeficit>True</checkMassDeficit>
  <recalibrationInPpm>True</recalibrationInPpm>
  <intensityDependentCalibration>False</intensityDependentCalibration>
  <minScoreForCalibration>70</minScoreForCalibration>
  <matchLibraryFile>False</matchLibraryFile>
  <libraryFile></libraryFile>
  <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
  <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
  <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
  <reporterMassTolerance>NaN</reporterMassTolerance>
  <reporterPif>NaN</reporterPif>
  <filterPif>False</filterPif>
  <reporterFraction>NaN</reporterFraction>
  <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
  <timsHalfWidth>0</timsHalfWidth>
  <timsStep>0</timsStep>
  <timsResolution>0</timsResolution>
  <timsMinMsmsIntensity>0</timsMinMsmsIntensity>
  <timsRemovePrecursor>True</timsRemovePrecursor>
  <timsIsobaricLabels>False</timsIsobaricLabels>
  <timsCollapseMsms>True</timsCollapseMsms>
  <crosslinkSearch>False</crosslinkSearch>
  <crossLinker></crossLinker>
  <minMatchXl>0</minMatchXl>
  <minPairedPepLenXl>6</minPairedPepLenXl>
  <crosslinkOnlyIntraProtein>False</crosslinkOnlyIntraProtein>
  <crosslinkMaxMonoUnsaturated>0</crosslinkMaxMonoUnsaturated>
  <crosslinkMaxMonoSaturated>0</crosslinkMaxMonoSaturated>
  <crosslinkMaxDiUnsaturated>0</crosslinkMaxDiUnsaturated>
  <crosslinkMaxDiSaturated>0</crosslinkMaxDiSaturated>
  <crosslinkUseSeparateFasta>False</crosslinkUseSeparateFasta>
  <crosslinkCleaveModifications>
  </crosslinkCleaveModifications>
  <crosslinkFastaFiles>
  </crosslinkFastaFiles>
  <crosslinkMode>PeptidesWithCleavedLinker</crosslinkMode>
  <peakRefinement>False</peakRefinement>
  <isobaricSumOverWindow>True</isobaricSumOverWindow>
  </parameterGroup>"
  
  
  parameterGroup_string['1.5.2.8'] <-
    "
    <parameterGroup>
         <maxCharge>7</maxCharge>
  <minPeakLen>2</minPeakLen>
  <useMs1Centroids>false</useMs1Centroids>
  <useMs2Centroids>false</useMs2Centroids>
  <cutPeaks>true</cutPeaks>
  <gapScans>1</gapScans>
  <minTime>NaN</minTime>
  <maxTime>NaN</maxTime>
  <matchType>MatchFromAndTo</matchType>
  <centroidMatchTol>8</centroidMatchTol>
  <centroidMatchTolInPpm>true</centroidMatchTolInPpm>
  <centroidHalfWidth>35</centroidHalfWidth>
  <centroidHalfWidthInPpm>true</centroidHalfWidthInPpm>
  <valleyFactor>1.4</valleyFactor>
  <advancedPeakSplitting>false</advancedPeakSplitting>
  <intensityThreshold>500</intensityThreshold>
  <msInstrument>0</msInstrument>
  <intensityDetermination>0</intensityDetermination>
  <labelMods>
  <string />
  </labelMods>
  <lfqMinEdgesPerNode>3</lfqMinEdgesPerNode>
  <lfqAvEdgesPerNode>6</lfqAvEdgesPerNode>
  <fastLfq>true</fastLfq>
  <lfqMinRatioCount>2</lfqMinRatioCount>
  <useNormRatiosForHybridLfq>true</useNormRatiosForHybridLfq>
  <maxLabeledAa>0</maxLabeledAa>
  <maxNmods>5</maxNmods>
  <maxMissedCleavages>2</maxMissedCleavages>
  <multiplicity>1</multiplicity>
<enzymeMode>%s</enzymeMode>
  <enzymes>
  %s
  </enzymes>
  <enzymesFirstSearch />
  <useEnzymeFirstSearch>false</useEnzymeFirstSearch>
  <useVariableModificationsFirstSearch>false</useVariableModificationsFirstSearch>
  <variableModifications>
  <string>Acetyl (Protein N-term)</string>
  <string>Oxidation (M)</string>
  </variableModifications>
  <isobaricLabels />
  <variableModificationsFirstSearch />
  <hasAdditionalVariableModifications>false</hasAdditionalVariableModifications>
  <additionalVariableModifications />
  <additionalVariableModificationProteins />
  <doMassFiltering>true</doMassFiltering>
  <firstSearchTol>20</firstSearchTol>
  <mainSearchTol>4.5</mainSearchTol>
  <searchTolInPpm>true</searchTolInPpm>
  <isotopeMatchTol>2</isotopeMatchTol>
  <isotopeMatchTolInPpm>true</isotopeMatchTolInPpm>
  <isotopeTimeCorrelation>0.6</isotopeTimeCorrelation>
  <theorIsotopeCorrelation>0.6</theorIsotopeCorrelation>
  <recalibrationInPpm>true</recalibrationInPpm>
  <intensityDependentCalibration>false</intensityDependentCalibration>
  <minScoreForCalibration>70</minScoreForCalibration>
  <matchLibraryFile>false</matchLibraryFile>
  <libraryFile />
  <matchLibraryMassTolPpm>0</matchLibraryMassTolPpm>
  <matchLibraryTimeTolMin>0</matchLibraryTimeTolMin>
  <matchLabelTimeTolMin>0</matchLabelTimeTolMin>
  <reporterMassTolerance>NaN</reporterMassTolerance>
  <reporterPif>NaN</reporterPif>
  <filterPif>false</filterPif>
  <reporterFraction>NaN</reporterFraction>
  <reporterBasePeakRatio>NaN</reporterBasePeakRatio>
  <lcmsRunType>Standard</lcmsRunType>
  <lfqMode>0</lfqMode>
  
  <enzymeModeFirstSearch>0</enzymeModeFirstSearch>
  </parameterGroup>
  "
  
  if(is.null(parameterGroup_string[version])){
    stop(version, " is unknown. Valid versions: \n",
         paste(names(parameterGroup_string), sep=", "))
  }
  
  par_groups <- paste(sapply(parameterGroups, function(settings) {
    sprintf(parameterGroup_string[[version]],
            settings['mode'],
            paste(sprintf('\n<string>%s</string>\n', 
                          switch(is.na(settings['enzyme']) + 1, 
                                 unlist(settings['enzyme']), 
                                 NULL)), 
                  collapse=''))
  }), sep='\n\n\n', collapse='\n\n')
  
  
  group_indices <- paste0("<int>", 0:(length(parameterGroups)-1), "</int>", collapse="\n")
  experiment_str <- paste0(rep("<string></string>", length(parameterGroups) ), collapse="\n", sep="\n")
  referenceChannel_str <- paste0(rep("<string></string>", length(parameterGroups) ), collapse="\n", sep="\n")
  fractions_str <- paste0(rep("<short>32767</short>", length(parameterGroups)), collapse="\n", sep="\n")
  ptms_str <- paste0(rep("<boolean>False</boolean>", length(parameterGroups)), collapse="\n", sep="\n")
  
  patterns <- getProtIdRegexFromFileName(fastaFiles)
  patterns <- gsub("\\\\", "\\\\\\\\", patterns) # mask \\ for substitution
  fasta_paths <- preparePathForSub(fastaFiles)
  
  if(version < '1.6'){
    fasta_paths <- paste0("<string>", fasta_paths, " </string>", collapse="\n")
  }else{
  fasta_paths <- paste0("<FastaFileInfo>
                        <fastaFilePath>", fasta_paths, "</fastaFilePath>
                        <identifierParseRule>", patterns, "</identifierParseRule>
                        <descriptionParseRule>>(.*)</descriptionParseRule>
                        <taxonomyParseRule></taxonomyParseRule>
                        <variationParseRule></variationParseRule>
                        <modificationParseRule></modificationParseRule>
                        <taxonomyId></taxonomyId>
                        </FastaFileInfo>", collapse="\n")
  }
  
  
  template <- sub("##__Parameter_Groups__##", par_groups, template)
  template <- sub("##__Group_Indices__##", group_indices, template)
  template <- sub("##__experiment__##", experiment_str, template)
  template <- sub("##__fractions__##", fractions_str, template)
  template <- sub("##__ptms__##", ptms_str, template)
  template <- sub("##__fastaFiles__##", fasta_paths, template)
  template <- sub("##__fixedFolder__##", fixedFolder, template)
  template <- sub("##__referenceChannel__##", referenceChannel_str, template)
  
  if(!is.null(rawFiles)){
    raw_paths <- preparePathForSub(rawFiles)
    raw_paths <- paste0("<string>", raw_paths, "</string>", collapse="\n")
    template <- sub("##__rawFiles__##", raw_paths, template)  
  }
  
  return(template)
}
#' normalize and prepare one or more paths for substitution into a string template
#' e.g. for Max Quant template string
#' @param paths paths to be prepared
#' @return prepared path(s)
#' @export
#' @examples
#' \dontrun{
#' preparePathForSub("test_dir/fasta_file.fasta")
#' }
preparePathForSub <- function(paths){
  paths <- normalizePath(paths)
  return(gsub("\\\\", "\\\\\\\\", paths))
}