Nothing
R/mq.fun.R
In mqqc: Quality control of LCMS derived proteomic data
Defines functions
mq.fun
mq.fun <-
function(filePath,folder,cores=1,SpeciesTable = T,templateFasta = list(REpar = "._.*_.*_PLACEHOLDER_"),placeholder = "PLACEHOLDER",skipUnknown = T,UseOwnXML = F, StandardIDs = c("BSA","ECstd"),GenDB = NULL,testFun = F,MQfilter = "all",GenericDBPath = NULL,MSFRAGGERpath = MSFRAGGERpath,MSFcores = MSFcores,case_sensitive_matching= F,MSFraggerFactor = 1,...){
RunFile <- T
continue = T
filePath <<- filePath
if(exists("db")){
if(length(db) == 0){
db <- NA
}
if(!file.exists(as.character(db))){
db <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "Ecoli.*.fasta$",full.name = T)
}
}else{
db <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "Ecoli.*.fasta$",full.name = T)
}
# creating string for system call of MQ
#check MQ path
checkMQ <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "MQpath",full.name = T)
if(length(checkMQ)==0 & .Platform$OS.type == "windows"){
cat("\rChoose MQ Directory!",rep(" ",100))
MQloop <- T
require(tcltk)
while(MQloop){
checkMQ <- tk_choose.dir( caption = "Please select folder containing MQ.")
checkMQ.bin <- list.files(paste(checkMQ.bin,"bin",sep = "/"),pattern = "MaxQuantCmd.exe",full.name = T)
if(length(checkMQ.bin) != 0){
write(checkMQ,file = paste(path.package("mqqc"),"data","MQpath",sep ="/"))
MQloop = F
}
}
}else{
try(checkMQ.bin <- readLines(checkMQ),silent = T)
}
# preparing XML
assign("filePath",filePath,envir = .GlobalEnv)
if(SpeciesTable){
species <- read.csv(paste(path.package("mqqc"),"data/MQQCspecies.txt",sep = "/"),sep = "\t")
regEx <- sapply(species$Abbreviation,function(x){gsub(placeholder,x, templateFasta$REpar,fixed = T)})
#regEx <- paste(regEx,"_",sep = "")
(fil <-paste(dirname(filePath),"RawFileName.txt",sep = "/"))
if(file.exists(fil)){
SearchString <- readLines(fil)[1]
}else{
SearchString <- basename(filePath)
}
SearchString <- gsub(".raw$","_raw", SearchString)
temp <- as.logical(sapply(regEx,grep, x = SearchString,ignore.case = !case_sensitive_matching)) #
temp[is.na(temp)] <- FALSE
continue = F
if(MQfilter == "all"){continue = T}
if(MQfilter == "db"){
cat("applying DB filter")
if(any(temp)){
continue = T
}
}
if(MQfilter == "std"){
cat("applying std filter")
if(any(species$Abbreviation[temp] == StandardIDs)){
continue = T
}
}
# cat("applying no filter")
if(!all(!temp)){
speciesUsed <- species[temp,]
GenDB <- NULL
}else{
if(continue){
speciesUsed <- species[species$Abbreviation == "default",]
if(is.na(speciesUsed$Fasta)){
speciesUsed$Fasta <- "THISISARANDOMPATHTHATSHOULDNTEXIST"
}
if(!file.exists(as.character(speciesUsed$Fasta))){
speciesUsed$Fasta <- GenericDBPath
GenDB <- GenericDBPath
}else{
GenDB <- speciesUsed$Fasta
}
}else{
speciesUsed <- NULL
}
}
# print("HUI")
# print(speciesUsed)
if(length(speciesUsed) > 0){
if(dim(speciesUsed)[1] > 1){
speciesUsed <- speciesUsed[1,]
}
xmlp <- as.character(speciesUsed$Xml)
if(length(xmlp) ==0|xmlp == "ToDo"){
UseOwnXML <- F
}else{ UseOwnXML <- file.exists(xmlp)}
if(UseOwnXML){
mqpar.name <- speciesUsed$Xml
}
try(tkdestroy(tempT),silent = T)
lastFile <- paste(basename(filePath),paste(unlist(speciesUsed[1,1:3]),collapse = "; "),sep = "\n")
try(tkControl(NA,NA,lastFile,htmloutPath = htmloutPath))
db <- speciesUsed$Fasta
tryError <- class(try(dbControl <- readLines(as.character(speciesUsed$Fasta),n= 1)))
if(tryError == "try-error" & !testFun){
if(skipUnknown){
try(write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
cat("\nError, Could not read fasta, run is aborted.\n")
write(c("Could not read Fasta",as.character(speciesUsed$Fasta)),file="error.txt")
RunFile <- F
SendMailFun(Message = paste("Hi\nyour file",basename(filePath),"was detected by MQQC.\nThere was a problem with the fasta-path which is attached to the parameter-ID.\nYour MQ-QC run was therefore aborted.\nSincerely\nYour MQQC") ,title = paste("MQQC warning:",basename(filePath)),filename = basename(filePath),RESettings = templateFasta)
}else{
cat("\nError, Could not read fasta, switched to default database.\n")
db <- NA
}
db <- list.files(path.package("mqqc"),pattern = "fasta",recursive = T,full.name =T)
}else{
try(write("",paste(dirname(filePath),"MQEnterTag",sep = "/")))
}
if(length(grep("/",db,fixed = T)) > 0){
db <- path.convert(db)
#try(db <- GenericDBPath)
}
}else{
if(skipUnknown){
db <- NA
print("SKIP")
}else{
# print("FOR")
if(length(GenDB) == 0){
GenDB <-NA
try(GenDB <- GenericDBPath)
}
db <- GenDB
}
}
}
if(!is.na(db)){
MQdbadder(checkMQ.bin,db)
MQdbadder(checkMQ.bin,"GenericDBFirstSearch.fasta")
mycofasta <- paste(path.package("mqqc"),"data/uniref90mycoOnlyName.fasta",sep = "/")
MQdbadder(checkMQ.bin,mycofasta)
#check DB
# if(!is.na(db)){
# dbXML <- readLines(paste(checkMQ.bin,"/bin/conf/databases.xml",sep = ""))
#
# CheckDB<- grep(paste("filename=\"",basename(db),sep = ""),dbXML)
# if(length(CheckDB) == 0){
# entry <- paste(" <databases filename=\"",basename(db),"\" search_expression=\"(.*)\" replacement_expression=\"%1\" />",sep = "")
# entrypoint <- grep("</Databases>",dbXML,ignore.case = T)
# XMLOUT <- c(dbXML[1:(entrypoint-1)],entry,dbXML[entrypoint:length(dbXML)])
# cat("\rWARNING: added DB to MQ config xml")
# }
# }
if(!UseOwnXML){
mqpar.name <- list.files(paste(path.package("mqqc"),"data",sep ="/"),"init_mqpar_lf.xml",full.name = T)
try(mqpar.name2 <- list.files(paste(path.package("mqqc"),"data",sep ="/"),"GDB.xml",full.name = T))
if(length(GenDB) > 0){
mqpar.name <- mqpar.name2
}
}
if(length(mqpar.name)!=0){
mqpar <- readLines(as.character(mqpar.name))
xmlNEW <- xml.replace(parent = c("filePaths"),insert = path.convert(filePath),mqpar)
if(length(speciesUsed$DependentPeptides) > 0){
if(speciesUsed$DependentPeptides){
mqparDP <- grep("<dependentPeptides>",xmlNEW)
xmlNEW[mqparDP] <- gsub(">false<",">true<",xmlNEW[mqparDP])
mqparDP <- grep("allPeptides",xmlNEW,ignore.case = T)
xmlNEW[mqparDP] <- gsub("writeAllPeptidesTable=\"false\"","writeAllPeptidesTable=\"true\"",xmlNEW[mqparDP])
}
}
MQVER <- gsub("[^0-9,.]", "",grep("maxQuantVersion",mqpar,value = T))
MQVER <- as.numeric(paste(unlist(strsplit(MQVER,".",fixed = T))[1:2],collapse = "."))
if(MQVER <1.4){
xmlNEW <- xml.replace(c("fileNames"),basename(filePath), xmlNEW)
xmlNEW <- xml.replace(c("parameterGroups"),rep(0,length(filePath)), xmlNEW,start.string = "<int>",end.string = "</int>")
# change processFolder
procFold <- grep("process",xmlNEW)
input.path <- (dirname((filePath)))
dir.create(paste(input.path,"combined/",sep = "/"))
dir.create(input.path <- paste(input.path,"combined/proc",sep = "/"))
input.path <- path.convert(input.path)
xmlNEW[procFold] <- gsub(paste("processFolder.*",sep =""),"",xmlNEW[procFold])
xmlNEW[procFold] <- paste(xmlNEW[procFold],paste("processFolder=\"",input.path,"\">",sep = ""))
# writing XML
}
if(!is.na(db)){
xmlNEW <- xml.replace("fastaFiles",c(db,gsub("/","\\\\",mycofasta)) , xmlNEW)
if(length(GenDB) > 0){
if(!is.na(GenDB)){
if(any(grepl("<fastaFilesFirstSearch />",xmlNEW))){
where <- grep("<fastaFilesFirstSearch />",xmlNEW)
xmlNEWstart <- xmlNEW[1:(where-1)]
xmlNEWend <- xmlNEW[(where+1):length(xmlNEW)]
xmlNEWmiddle <- xmlNEW[where]
xmlNEWmiddle <- c(gsub(" />",">",xmlNEWmiddle,fixed = T))
xmlNEWmiddle <- c(xmlNEWmiddle," <string>/bla.fasta</string>" ,gsub("<fasta","</fasta",xmlNEWmiddle))
xmlNEW <- c(xmlNEWstart,xmlNEWmiddle,xmlNEWend)
}
xmlNEW<- xml.replace("fastaFilesFirstSearch",gsub("GenericDB.fasta$", "GenericDBFirstSearch.fasta",db), xmlNEW)
}
}
}
}
if(speciesUsed$Abbreviation == "default"&!file.exists(as.character(speciesUsed$Fasta))){
xmlNEW<- gsub("<proteinFdr>.*.</proteinFdr>","<proteinFdr>1</proteinFdr>",xmlNEW)
xmlNEW<- gsub("<peptideFdr>.*.</peptideFdr>","<peptideFdr>0.5</peptideFdr>",xmlNEW)
#grep("peptideFdr",xmlNEW,value = T)
}
if(RunFile){
write(xmlNEW,xml.path <- paste(dirname(filePath),"mqpar.xml",sep = "/"))
if(file.exists(db)){
# try(CheckFastaDB(checkMQ.bin,basename(db)))
}
threads <- 1
MQ <- "MaxQuantCmd.exe"
if(MQVER >1.4){
threads = ""
}
MQcmd <- paste("\"",checkMQ.bin,"/bin/",MQ,"\" \"", xml.path,"\" ",threads,sep = "")
# MQcmd <- path.convert(MQcmd)
print(continue)
# return(xmlNEW[2])
cores <- as.numeric(cores)
if(is.na(cores[1])){cores <- 1;print("Warning, set number of threads to 1.")}
print(db)
if(file.exists(MSFRAGGERpath)){
MSFcmd <- ""
try({
DB <- db # taken from MQstarter
andromeda <- dirname(filePath) # path with temp.raw, script will select all rawfiles
write(rscript_msf(),msfpath<-paste(dirname(filePath),"msfragger_rscript.R",sep= "/"))
Rscript_system<- "rscript"
MSFcmd <- paste(Rscript_system,msfpath,MSFRAGGERpath,DB,andromeda,MSFcores,dirname(filePath))
write(MSFcmd,paste(dirname(filePath),"msfragger_cmd",sep= "/"))
# system(MSFcmd,wait=F)
})
MQcmd <- paste(MQcmd,MSFcmd,sep= "###")
}else{
print("MSFRAGGER not found. No open search.")
}
if(continue){
try(MQmanager(MQcmd,folder,cores =cores,msfraggerFactor = MSFraggerFactor))
}
try( write(MQcmd,paste(dirname(filePath),"MQQC_MQcmd.txt",sep = "/")))
#initialize MSFRAGGERRUN:
#write("msfragger_started",paste(dirname(x),"msfragger_started",sep = "/"))
# MSFRAGGERpath
# MSFcores
}else{
print("Error in MQ start. No XML provided.")
if(!file.exists(paste(dirname(filePath),"DeleteTag",sep = "/"))){
try(write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
SendMailFun(Message = paste("Hi\nyour file",basename(filePath),"was detected by MQQC.\nThere was no match to any parameter ID.") ,title = paste("MQQC warning:",basename(filePath)),filename = basename(filePath),RESettings = templateFasta)
}
RunFile <- F
try( write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
}
}else{
cat("no valid DB Found")
if(!file.exists(paste(dirname(filePath),"DeleteTag",sep = "/"))){
try(write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
print(templateFasta)
SendMailFun(Message = paste("Hi\nyour file",basename(filePath),"was detected by MQQC.\nThere was no match to any parameter ID.") ,title = paste("MQQC warning:",basename(filePath)),filename = basename(filePath),RESettings = templateFasta)
}
RunFile <- F
}
}
# filePath <- "hucke_111111_HZ_EC.raw"
# mq.fun(filePath,MQfilter = "std",templateFasta = RESettings)
#tryError <- class(try(mqStarter(temp.batch.n=temp.batch.n,folder = folder,cores = cores, SpeciesTable = SpeciesTable, templateFasta = RESettings, placeholder = placeholder,InfoString = "_RmqqcFile_", StandardIDs = StandardIDs,MQfilter = MQfilter)))
# mq.fun("C:/AG Selbach/mqqc/Statler_20160723_HZ_BSA_FakeFileraw_folderX2016.07.22.13.49.44/Statler_20160723_HZ_BSA_FakeFile.raw",folder = folder)
# GenericDBPath
# LoadSettings(cores=1,SpeciesTable = T,templateFasta = list(REpar = "._.*_.*_PLACEHOLDER_"),placeholder = "PLACEHOLDER",skipUnknown = T,UseOwnXML = F, StandardIDs = StandardIDs,GenDB = NULL,testFun = F)
# mq.fun(filePath="./Tiffy_20151005_HZ_EC_test.raw",folder = folder,StandardIDs = c("ECstd","BSA"),testFun = F )
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Defines functions mq.fun
mq.fun <-
function(filePath,folder,cores=1,SpeciesTable = T,templateFasta = list(REpar = "._.*_.*_PLACEHOLDER_"),placeholder = "PLACEHOLDER",skipUnknown = T,UseOwnXML = F, StandardIDs = c("BSA","ECstd"),GenDB = NULL,testFun = F,MQfilter = "all",GenericDBPath = NULL,MSFRAGGERpath = MSFRAGGERpath,MSFcores = MSFcores,case_sensitive_matching= F,MSFraggerFactor = 1,...){
RunFile <- T
continue = T
filePath <<- filePath
if(exists("db")){
if(length(db) == 0){
db <- NA
}
if(!file.exists(as.character(db))){
db <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "Ecoli.*.fasta$",full.name = T)
}
}else{
db <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "Ecoli.*.fasta$",full.name = T)
}
# creating string for system call of MQ
#check MQ path
checkMQ <- list.files(paste(path.package("mqqc"),"data",sep ="/"),pattern = "MQpath",full.name = T)
if(length(checkMQ)==0 & .Platform$OS.type == "windows"){
cat("\rChoose MQ Directory!",rep(" ",100))
MQloop <- T
require(tcltk)
while(MQloop){
checkMQ <- tk_choose.dir( caption = "Please select folder containing MQ.")
checkMQ.bin <- list.files(paste(checkMQ.bin,"bin",sep = "/"),pattern = "MaxQuantCmd.exe",full.name = T)
if(length(checkMQ.bin) != 0){
write(checkMQ,file = paste(path.package("mqqc"),"data","MQpath",sep ="/"))
MQloop = F
}
}
}else{
try(checkMQ.bin <- readLines(checkMQ),silent = T)
}
# preparing XML
assign("filePath",filePath,envir = .GlobalEnv)
if(SpeciesTable){
species <- read.csv(paste(path.package("mqqc"),"data/MQQCspecies.txt",sep = "/"),sep = "\t")
regEx <- sapply(species$Abbreviation,function(x){gsub(placeholder,x, templateFasta$REpar,fixed = T)})
#regEx <- paste(regEx,"_",sep = "")
(fil <-paste(dirname(filePath),"RawFileName.txt",sep = "/"))
if(file.exists(fil)){
SearchString <- readLines(fil)[1]
}else{
SearchString <- basename(filePath)
}
SearchString <- gsub(".raw$","_raw", SearchString)
temp <- as.logical(sapply(regEx,grep, x = SearchString,ignore.case = !case_sensitive_matching)) #
temp[is.na(temp)] <- FALSE
continue = F
if(MQfilter == "all"){continue = T}
if(MQfilter == "db"){
cat("applying DB filter")
if(any(temp)){
continue = T
}
}
if(MQfilter == "std"){
cat("applying std filter")
if(any(species$Abbreviation[temp] == StandardIDs)){
continue = T
}
}
# cat("applying no filter")
if(!all(!temp)){
speciesUsed <- species[temp,]
GenDB <- NULL
}else{
if(continue){
speciesUsed <- species[species$Abbreviation == "default",]
if(is.na(speciesUsed$Fasta)){
speciesUsed$Fasta <- "THISISARANDOMPATHTHATSHOULDNTEXIST"
}
if(!file.exists(as.character(speciesUsed$Fasta))){
speciesUsed$Fasta <- GenericDBPath
GenDB <- GenericDBPath
}else{
GenDB <- speciesUsed$Fasta
}
}else{
speciesUsed <- NULL
}
}
# print("HUI")
# print(speciesUsed)
if(length(speciesUsed) > 0){
if(dim(speciesUsed)[1] > 1){
speciesUsed <- speciesUsed[1,]
}
xmlp <- as.character(speciesUsed$Xml)
if(length(xmlp) ==0|xmlp == "ToDo"){
UseOwnXML <- F
}else{ UseOwnXML <- file.exists(xmlp)}
if(UseOwnXML){
mqpar.name <- speciesUsed$Xml
}
try(tkdestroy(tempT),silent = T)
lastFile <- paste(basename(filePath),paste(unlist(speciesUsed[1,1:3]),collapse = "; "),sep = "\n")
try(tkControl(NA,NA,lastFile,htmloutPath = htmloutPath))
db <- speciesUsed$Fasta
tryError <- class(try(dbControl <- readLines(as.character(speciesUsed$Fasta),n= 1)))
if(tryError == "try-error" & !testFun){
if(skipUnknown){
try(write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
cat("\nError, Could not read fasta, run is aborted.\n")
write(c("Could not read Fasta",as.character(speciesUsed$Fasta)),file="error.txt")
RunFile <- F
SendMailFun(Message = paste("Hi\nyour file",basename(filePath),"was detected by MQQC.\nThere was a problem with the fasta-path which is attached to the parameter-ID.\nYour MQ-QC run was therefore aborted.\nSincerely\nYour MQQC") ,title = paste("MQQC warning:",basename(filePath)),filename = basename(filePath),RESettings = templateFasta)
}else{
cat("\nError, Could not read fasta, switched to default database.\n")
db <- NA
}
db <- list.files(path.package("mqqc"),pattern = "fasta",recursive = T,full.name =T)
}else{
try(write("",paste(dirname(filePath),"MQEnterTag",sep = "/")))
}
if(length(grep("/",db,fixed = T)) > 0){
db <- path.convert(db)
#try(db <- GenericDBPath)
}
}else{
if(skipUnknown){
db <- NA
print("SKIP")
}else{
# print("FOR")
if(length(GenDB) == 0){
GenDB <-NA
try(GenDB <- GenericDBPath)
}
db <- GenDB
}
}
}
if(!is.na(db)){
MQdbadder(checkMQ.bin,db)
MQdbadder(checkMQ.bin,"GenericDBFirstSearch.fasta")
mycofasta <- paste(path.package("mqqc"),"data/uniref90mycoOnlyName.fasta",sep = "/")
MQdbadder(checkMQ.bin,mycofasta)
#check DB
# if(!is.na(db)){
# dbXML <- readLines(paste(checkMQ.bin,"/bin/conf/databases.xml",sep = ""))
#
# CheckDB<- grep(paste("filename=\"",basename(db),sep = ""),dbXML)
# if(length(CheckDB) == 0){
# entry <- paste(" <databases filename=\"",basename(db),"\" search_expression=\"(.*)\" replacement_expression=\"%1\" />",sep = "")
# entrypoint <- grep("</Databases>",dbXML,ignore.case = T)
# XMLOUT <- c(dbXML[1:(entrypoint-1)],entry,dbXML[entrypoint:length(dbXML)])
# cat("\rWARNING: added DB to MQ config xml")
# }
# }
if(!UseOwnXML){
mqpar.name <- list.files(paste(path.package("mqqc"),"data",sep ="/"),"init_mqpar_lf.xml",full.name = T)
try(mqpar.name2 <- list.files(paste(path.package("mqqc"),"data",sep ="/"),"GDB.xml",full.name = T))
if(length(GenDB) > 0){
mqpar.name <- mqpar.name2
}
}
if(length(mqpar.name)!=0){
mqpar <- readLines(as.character(mqpar.name))
xmlNEW <- xml.replace(parent = c("filePaths"),insert = path.convert(filePath),mqpar)
if(length(speciesUsed$DependentPeptides) > 0){
if(speciesUsed$DependentPeptides){
mqparDP <- grep("<dependentPeptides>",xmlNEW)
xmlNEW[mqparDP] <- gsub(">false<",">true<",xmlNEW[mqparDP])
mqparDP <- grep("allPeptides",xmlNEW,ignore.case = T)
xmlNEW[mqparDP] <- gsub("writeAllPeptidesTable=\"false\"","writeAllPeptidesTable=\"true\"",xmlNEW[mqparDP])
}
}
MQVER <- gsub("[^0-9,.]", "",grep("maxQuantVersion",mqpar,value = T))
MQVER <- as.numeric(paste(unlist(strsplit(MQVER,".",fixed = T))[1:2],collapse = "."))
if(MQVER <1.4){
xmlNEW <- xml.replace(c("fileNames"),basename(filePath), xmlNEW)
xmlNEW <- xml.replace(c("parameterGroups"),rep(0,length(filePath)), xmlNEW,start.string = "<int>",end.string = "</int>")
# change processFolder
procFold <- grep("process",xmlNEW)
input.path <- (dirname((filePath)))
dir.create(paste(input.path,"combined/",sep = "/"))
dir.create(input.path <- paste(input.path,"combined/proc",sep = "/"))
input.path <- path.convert(input.path)
xmlNEW[procFold] <- gsub(paste("processFolder.*",sep =""),"",xmlNEW[procFold])
xmlNEW[procFold] <- paste(xmlNEW[procFold],paste("processFolder=\"",input.path,"\">",sep = ""))
# writing XML
}
if(!is.na(db)){
xmlNEW <- xml.replace("fastaFiles",c(db,gsub("/","\\\\",mycofasta)) , xmlNEW)
if(length(GenDB) > 0){
if(!is.na(GenDB)){
if(any(grepl("<fastaFilesFirstSearch />",xmlNEW))){
where <- grep("<fastaFilesFirstSearch />",xmlNEW)
xmlNEWstart <- xmlNEW[1:(where-1)]
xmlNEWend <- xmlNEW[(where+1):length(xmlNEW)]
xmlNEWmiddle <- xmlNEW[where]
xmlNEWmiddle <- c(gsub(" />",">",xmlNEWmiddle,fixed = T))
xmlNEWmiddle <- c(xmlNEWmiddle," <string>/bla.fasta</string>" ,gsub("<fasta","</fasta",xmlNEWmiddle))
xmlNEW <- c(xmlNEWstart,xmlNEWmiddle,xmlNEWend)
}
xmlNEW<- xml.replace("fastaFilesFirstSearch",gsub("GenericDB.fasta$", "GenericDBFirstSearch.fasta",db), xmlNEW)
}
}
}
}
if(speciesUsed$Abbreviation == "default"&!file.exists(as.character(speciesUsed$Fasta))){
xmlNEW<- gsub("<proteinFdr>.*.</proteinFdr>","<proteinFdr>1</proteinFdr>",xmlNEW)
xmlNEW<- gsub("<peptideFdr>.*.</peptideFdr>","<peptideFdr>0.5</peptideFdr>",xmlNEW)
#grep("peptideFdr",xmlNEW,value = T)
}
if(RunFile){
write(xmlNEW,xml.path <- paste(dirname(filePath),"mqpar.xml",sep = "/"))
if(file.exists(db)){
# try(CheckFastaDB(checkMQ.bin,basename(db)))
}
threads <- 1
MQ <- "MaxQuantCmd.exe"
if(MQVER >1.4){
threads = ""
}
MQcmd <- paste("\"",checkMQ.bin,"/bin/",MQ,"\" \"", xml.path,"\" ",threads,sep = "")
# MQcmd <- path.convert(MQcmd)
print(continue)
# return(xmlNEW[2])
cores <- as.numeric(cores)
if(is.na(cores[1])){cores <- 1;print("Warning, set number of threads to 1.")}
print(db)
if(file.exists(MSFRAGGERpath)){
MSFcmd <- ""
try({
DB <- db # taken from MQstarter
andromeda <- dirname(filePath) # path with temp.raw, script will select all rawfiles
write(rscript_msf(),msfpath<-paste(dirname(filePath),"msfragger_rscript.R",sep= "/"))
Rscript_system<- "rscript"
MSFcmd <- paste(Rscript_system,msfpath,MSFRAGGERpath,DB,andromeda,MSFcores,dirname(filePath))
write(MSFcmd,paste(dirname(filePath),"msfragger_cmd",sep= "/"))
# system(MSFcmd,wait=F)
})
MQcmd <- paste(MQcmd,MSFcmd,sep= "###")
}else{
print("MSFRAGGER not found. No open search.")
}
if(continue){
try(MQmanager(MQcmd,folder,cores =cores,msfraggerFactor = MSFraggerFactor))
}
try( write(MQcmd,paste(dirname(filePath),"MQQC_MQcmd.txt",sep = "/")))
#initialize MSFRAGGERRUN:
#write("msfragger_started",paste(dirname(x),"msfragger_started",sep = "/"))
# MSFRAGGERpath
# MSFcores
}else{
print("Error in MQ start. No XML provided.")
if(!file.exists(paste(dirname(filePath),"DeleteTag",sep = "/"))){
try(write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
SendMailFun(Message = paste("Hi\nyour file",basename(filePath),"was detected by MQQC.\nThere was no match to any parameter ID.") ,title = paste("MQQC warning:",basename(filePath)),filename = basename(filePath),RESettings = templateFasta)
}
RunFile <- F
try( write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
}
}else{
cat("no valid DB Found")
if(!file.exists(paste(dirname(filePath),"DeleteTag",sep = "/"))){
try(write.csv("",paste(dirname(filePath),"DeleteTag",sep = "/")))
print(templateFasta)
SendMailFun(Message = paste("Hi\nyour file",basename(filePath),"was detected by MQQC.\nThere was no match to any parameter ID.") ,title = paste("MQQC warning:",basename(filePath)),filename = basename(filePath),RESettings = templateFasta)
}
RunFile <- F
}
}
# filePath <- "hucke_111111_HZ_EC.raw"
# mq.fun(filePath,MQfilter = "std",templateFasta = RESettings)
#tryError <- class(try(mqStarter(temp.batch.n=temp.batch.n,folder = folder,cores = cores, SpeciesTable = SpeciesTable, templateFasta = RESettings, placeholder = placeholder,InfoString = "_RmqqcFile_", StandardIDs = StandardIDs,MQfilter = MQfilter)))
# mq.fun("C:/AG Selbach/mqqc/Statler_20160723_HZ_BSA_FakeFileraw_folderX2016.07.22.13.49.44/Statler_20160723_HZ_BSA_FakeFile.raw",folder = folder)
# GenericDBPath
# LoadSettings(cores=1,SpeciesTable = T,templateFasta = list(REpar = "._.*_.*_PLACEHOLDER_"),placeholder = "PLACEHOLDER",skipUnknown = T,UseOwnXML = F, StandardIDs = StandardIDs,GenDB = NULL,testFun = F)
# mq.fun(filePath="./Tiffy_20151005_HZ_EC_test.raw",folder = folder,StandardIDs = c("ECstd","BSA"),testFun = F )
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