R/validateMassBank.R
In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records
Defines functions
.unitTestRMB2
.unitTestmzR
smiles2mass
validate
Documented in
smiles2mass
validate
#' Validate MassBank records with a set of Unit tests
#'
#' Validates a plain text MassBank record, or recursively all
#' records within a directory. The Unit Tests to be used are
#' installed in RMassBank/inst/validationTests and currently include
#' checks for NAs, peaks versus precursor, precursor mz,
#' precursor type, SMILES vs exact mass, total intensities and
#' title versus type. The validation report is saved as
#' "report.html" in the working directory.
#'
#' @aliases validate
#' @usage validate(path, simple = TRUE)
#' @param path The filepath to a single record, or a directory to search recursively
#' @param simple If TRUE the function creates a simpler form of the RUnit .html report, better readable for humans. If FALSE it returns the unchanged RUnit report.
#' @examples
#' \dontrun{
#' validate("/tmp/MassBank/OpenData/record/")
#' }
#' @export
validate <- function(path, simple = TRUE) {
requireNamespace("RUnit",quietly=TRUE)
# Is the argument a directory?
# If yes, list the files
RMassBank.env$testnumber <- 1
if(file.info(path[1])$isdir){
Files <- list.files(path = path,
recursive=TRUE,
full.names = TRUE)
} else {Files <- path}
# Parsing with the help the parseMassBank-function
RMassBank.env$mb <- lapply(Files,parseMassBank)
# Test RMassBank Objects with RUnit
# This loop creates the tests and defines one test suite for every record
tests <- list()
for(i in 1:length(RMassBank.env$mb)){
if(RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS2" || RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS"){
tests[[i]] <- RUnit::defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "runit.MS2.test.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
} else{
tests[[i]] <- RUnit::defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "^runit.MSn.test.[rR]$",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
}
}
print("Starting Tests")
# Testing the list of Testsuites
testData <- suppressWarnings(RUnit::runTestSuite(tests,verbose=0))
# Prints the HTML-record
RUnit::printHTMLProtocol(testData, fileName = paste0(getwd(),"/report.html"))
if(simple){
fileConnection <- file(paste0(getwd(),"/report.html"), open = "r")
htmlFile <- readLines(fileConnection)
close(fileConnection)
htmlFile <- gsub(">test.NA", ">No NAs contained in peak list", htmlFile)
htmlFile <- gsub(">test.peaksvsprecursor", ">One peak m/z with no noticable difference from the precursor mass", htmlFile)
htmlFile <- gsub(">test.precursormz", ">Mass of precursor m/z possible with given mass and type", htmlFile)
htmlFile <- gsub(">test.PrecursorType", ">Precursor type valid", htmlFile)
htmlFile <- gsub(">test.smilesvsexactmass", ">Smiles code represents a molecule with specified exact mass", htmlFile)
htmlFile <- gsub(">test.sumintensities", ">All intensies greater than zero", htmlFile)
htmlFile <- gsub(">test.TitleVsType", ">Precursor type are the same in the title and in the document", htmlFile)
htmlFile <- gsub("\\(1 checks\\)", "", htmlFile)
htmlFile <- gsub("\\({1}.{1,6}seconds\\)", "", htmlFile)
htmlFile <- gsub("Test Suite: ", "", htmlFile)
htmlFile <- gsub("h5", "h2", htmlFile)
##Remove ending
poshr <- grep("<hr>", htmlFile, fixed=TRUE)
poshr <- poshr[length(poshr)]
htmlFile <- htmlFile[1:(poshr)]
ullines <- grep("<ul>", htmlFile)
htmlFile[ullines] <- gsub("</a><ul>", "</a></li>", htmlFile[ullines])
htmlFile[ullines] <- gsub("</li></ul></li></ul>", "</li></ul>", htmlFile[ullines])
htmlFile[ullines] <- gsub('<li><a href=".+">Test file: runit.MS2.test.R</a></li>', "", htmlFile[ullines])
htmlFile[ullines] <- gsub('</a>.+RMassBank/validationTests<br/>',"</a>", htmlFile[ullines])
##Remove superfluous information
htmlFile <- gsub("Test function regexp: ^test.+<br/>Test file regexp: runit.MS2.test.R<br/>Involved directory:<br/>", "", htmlFile, fixed=TRUE)
fileConnection <- file(paste0(getwd(),"/report.html"), open = "w")
writeLines(htmlFile, fileConnection)
close(fileConnection)
}
print(paste("Report for the file(s) finished"))
}
#' Calculate the mass from a SMILES-String
#'
#' Uses a SMILES-String to calculate the mass using rcdk-integrated functions.
#'
#' @aliases smiles2mass
#' @usage smiles2mass(SMILES)
#' @param SMILES A String-object representing a SMILES
#' @return The calculated mass of the given SMILES-Formula
#' @author Erik Mueller
#' @examples \dontrun{
#' smiles2mass("CC(=O)NC(C(O)1)C(O)C(OC(O2)C(O)C(OC(O3)C(O)C(O)C(O)C(CO)3)C(O)C(CO)2)C(CO)O1")
#' }
#' @export
smiles2mass <- function(SMILES){
massfromformula <- parse.smiles(SMILES)[[1]]
do.typing(massfromformula)
do.aromaticity(massfromformula)
convert.implicit.to.explicit(massfromformula)
do.isotopes(massfromformula)
mass <- get.exact.mass(massfromformula)
return(mass)
}
.unitTestmzR <- function(WD=getwd()){
requireNamespace("RUnit",quietly=TRUE)
requireNamespace("RMassBankData",quietly=TRUE)
oldwd <- getwd()
setwd(WD)
w <- newMsmsWorkspace()
RmbDefaultSettings()
files <- list.files(system.file("spectra", package="RMassBankData"),
".mzML", full.names = TRUE)
w@files <- files
loadList(system.file("list/NarcoticsDataset.csv",
package="RMassBankData"))
w <- msmsWorkflow(w, mode="pH", steps=c(1:4), archivename =
"pH_narcotics")
storedW <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF.RData",
package="RMassBankData"))
storedW <- msmsWorkflow(storedW, mode="pH", steps=4)
w@rc <- storedW@rc
w@rc.ms1 <- storedW@rc.ms1
w <- msmsWorkflow(w, mode="pH", steps=4, archivename =
"pH_narcotics", newRecalibration = FALSE)
w <- msmsWorkflow(w, mode="pH", steps=c(5:8), archivename =
"pH_narcotics")
mb <- newMbWorkspace(w)
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists_incomplete",
package="RMassBankData"))
mb <- mbWorkflow(mb, infolist_path="./Narcotics_infolist.csv")
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData"))
mb <- mbWorkflow(mb)
testSuite <- RUnit::defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testSuite2 <- RUnit::defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
file.remove(c("pH_narcotics_Failpeaks.csv","pH_narcotics.RData","pH_narcotics_RA.RData","pH_narcotics_RF.RData"))
RUnit::printTextProtocol(testData)
RUnit::printTextProtocol(testData2)
setwd(oldwd)
return(testData)
}
.unitTestRMB2 <- function(WD=getwd()){
requireNamespace("RUnit",quietly=TRUE)
requireNamespace("RMassBankData",quietly=TRUE)
oldwd <- getwd()
setwd(WD)
w <- newMsmsWorkspace()
RmbDefaultSettings()
files <- list.files(system.file("spectra", package="RMassBankData"),
".mzML", full.names = TRUE)
w@files <- files
loadList(system.file("list/NarcoticsDataset.csv",
package="RMassBankData"))
w <- msmsWorkflow(w, mode="pH", steps=c(1), archivename =
"pH_narcotics")
w <- newStep2WorkFlow(w, mode="pH", analyzeMethod="formula")
w <- msmsWorkflow(w, mode="pH", steps=c(3:4), archivename =
"pH_narcotics")
storedW <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF.RData",
package="RMassBankData"))
storedW <- msmsWorkflow(storedW, mode="pH", steps=4)
w@rc <- storedW@rc
w@rc.ms1 <- storedW@rc.ms1
w <- msmsWorkflow(w, mode="pH", steps=4, archivename =
"pH_narcotics", newRecalibration = FALSE)
w <- msmsWorkflow(w, mode="pH", steps=c(5:8), archivename =
"pH_narcotics")
mb <- newMbWorkspace(w)
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists_incomplete",
package="RMassBankData"))
mb <- mbWorkflow(mb, infolist_path="./Narcotics_infolist.csv")
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData"))
mb <- mbWorkflow(mb)
testSuite <- RUnit::defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testSuite2 <- RUnit::defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
file.remove(c("pH_narcotics_Failpeaks.csv","pH_narcotics.RData","pH_narcotics_RA.RData","pH_narcotics_RF.RData"))
RUnit::printTextProtocol(testData)
RUnit::printTextProtocol(testData2)
setwd(oldwd)
return(testData)
}
sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.
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Defines functions .unitTestRMB2 .unitTestmzR smiles2mass validate
Documented in smiles2mass validate
#' Validate MassBank records with a set of Unit tests
#'
#' Validates a plain text MassBank record, or recursively all
#' records within a directory. The Unit Tests to be used are
#' installed in RMassBank/inst/validationTests and currently include
#' checks for NAs, peaks versus precursor, precursor mz,
#' precursor type, SMILES vs exact mass, total intensities and
#' title versus type. The validation report is saved as
#' "report.html" in the working directory.
#'
#' @aliases validate
#' @usage validate(path, simple = TRUE)
#' @param path The filepath to a single record, or a directory to search recursively
#' @param simple If TRUE the function creates a simpler form of the RUnit .html report, better readable for humans. If FALSE it returns the unchanged RUnit report.
#' @examples
#' \dontrun{
#' validate("/tmp/MassBank/OpenData/record/")
#' }
#' @export
validate <- function(path, simple = TRUE) {
requireNamespace("RUnit",quietly=TRUE)
# Is the argument a directory?
# If yes, list the files
RMassBank.env$testnumber <- 1
if(file.info(path[1])$isdir){
Files <- list.files(path = path,
recursive=TRUE,
full.names = TRUE)
} else {Files <- path}
# Parsing with the help the parseMassBank-function
RMassBank.env$mb <- lapply(Files,parseMassBank)
# Test RMassBank Objects with RUnit
# This loop creates the tests and defines one test suite for every record
tests <- list()
for(i in 1:length(RMassBank.env$mb)){
if(RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS2" || RMassBank.env$mb[[i]]@compiled_ok[[1]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']] == "MS"){
tests[[i]] <- RUnit::defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "runit.MS2.test.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
} else{
tests[[i]] <- RUnit::defineTestSuite(Files[i], dirs = system.file(package="RMassBank", "validationTests"), testFileRegexp = "^runit.MSn.test.[rR]$",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
}
}
print("Starting Tests")
# Testing the list of Testsuites
testData <- suppressWarnings(RUnit::runTestSuite(tests,verbose=0))
# Prints the HTML-record
RUnit::printHTMLProtocol(testData, fileName = paste0(getwd(),"/report.html"))
if(simple){
fileConnection <- file(paste0(getwd(),"/report.html"), open = "r")
htmlFile <- readLines(fileConnection)
close(fileConnection)
htmlFile <- gsub(">test.NA", ">No NAs contained in peak list", htmlFile)
htmlFile <- gsub(">test.peaksvsprecursor", ">One peak m/z with no noticable difference from the precursor mass", htmlFile)
htmlFile <- gsub(">test.precursormz", ">Mass of precursor m/z possible with given mass and type", htmlFile)
htmlFile <- gsub(">test.PrecursorType", ">Precursor type valid", htmlFile)
htmlFile <- gsub(">test.smilesvsexactmass", ">Smiles code represents a molecule with specified exact mass", htmlFile)
htmlFile <- gsub(">test.sumintensities", ">All intensies greater than zero", htmlFile)
htmlFile <- gsub(">test.TitleVsType", ">Precursor type are the same in the title and in the document", htmlFile)
htmlFile <- gsub("\\(1 checks\\)", "", htmlFile)
htmlFile <- gsub("\\({1}.{1,6}seconds\\)", "", htmlFile)
htmlFile <- gsub("Test Suite: ", "", htmlFile)
htmlFile <- gsub("h5", "h2", htmlFile)
##Remove ending
poshr <- grep("<hr>", htmlFile, fixed=TRUE)
poshr <- poshr[length(poshr)]
htmlFile <- htmlFile[1:(poshr)]
ullines <- grep("<ul>", htmlFile)
htmlFile[ullines] <- gsub("</a><ul>", "</a></li>", htmlFile[ullines])
htmlFile[ullines] <- gsub("</li></ul></li></ul>", "</li></ul>", htmlFile[ullines])
htmlFile[ullines] <- gsub('<li><a href=".+">Test file: runit.MS2.test.R</a></li>', "", htmlFile[ullines])
htmlFile[ullines] <- gsub('</a>.+RMassBank/validationTests<br/>',"</a>", htmlFile[ullines])
##Remove superfluous information
htmlFile <- gsub("Test function regexp: ^test.+<br/>Test file regexp: runit.MS2.test.R<br/>Involved directory:<br/>", "", htmlFile, fixed=TRUE)
fileConnection <- file(paste0(getwd(),"/report.html"), open = "w")
writeLines(htmlFile, fileConnection)
close(fileConnection)
}
print(paste("Report for the file(s) finished"))
}
#' Calculate the mass from a SMILES-String
#'
#' Uses a SMILES-String to calculate the mass using rcdk-integrated functions.
#'
#' @aliases smiles2mass
#' @usage smiles2mass(SMILES)
#' @param SMILES A String-object representing a SMILES
#' @return The calculated mass of the given SMILES-Formula
#' @author Erik Mueller
#' @examples \dontrun{
#' smiles2mass("CC(=O)NC(C(O)1)C(O)C(OC(O2)C(O)C(OC(O3)C(O)C(O)C(O)C(CO)3)C(O)C(CO)2)C(CO)O1")
#' }
#' @export
smiles2mass <- function(SMILES){
massfromformula <- parse.smiles(SMILES)[[1]]
do.typing(massfromformula)
do.aromaticity(massfromformula)
convert.implicit.to.explicit(massfromformula)
do.isotopes(massfromformula)
mass <- get.exact.mass(massfromformula)
return(mass)
}
.unitTestmzR <- function(WD=getwd()){
requireNamespace("RUnit",quietly=TRUE)
requireNamespace("RMassBankData",quietly=TRUE)
oldwd <- getwd()
setwd(WD)
w <- newMsmsWorkspace()
RmbDefaultSettings()
files <- list.files(system.file("spectra", package="RMassBankData"),
".mzML", full.names = TRUE)
w@files <- files
loadList(system.file("list/NarcoticsDataset.csv",
package="RMassBankData"))
w <- msmsWorkflow(w, mode="pH", steps=c(1:4), archivename =
"pH_narcotics")
storedW <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF.RData",
package="RMassBankData"))
storedW <- msmsWorkflow(storedW, mode="pH", steps=4)
w@rc <- storedW@rc
w@rc.ms1 <- storedW@rc.ms1
w <- msmsWorkflow(w, mode="pH", steps=4, archivename =
"pH_narcotics", newRecalibration = FALSE)
w <- msmsWorkflow(w, mode="pH", steps=c(5:8), archivename =
"pH_narcotics")
mb <- newMbWorkspace(w)
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists_incomplete",
package="RMassBankData"))
mb <- mbWorkflow(mb, infolist_path="./Narcotics_infolist.csv")
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData"))
mb <- mbWorkflow(mb)
testSuite <- RUnit::defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testSuite2 <- RUnit::defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
file.remove(c("pH_narcotics_Failpeaks.csv","pH_narcotics.RData","pH_narcotics_RA.RData","pH_narcotics_RF.RData"))
RUnit::printTextProtocol(testData)
RUnit::printTextProtocol(testData2)
setwd(oldwd)
return(testData)
}
.unitTestRMB2 <- function(WD=getwd()){
requireNamespace("RUnit",quietly=TRUE)
requireNamespace("RMassBankData",quietly=TRUE)
oldwd <- getwd()
setwd(WD)
w <- newMsmsWorkspace()
RmbDefaultSettings()
files <- list.files(system.file("spectra", package="RMassBankData"),
".mzML", full.names = TRUE)
w@files <- files
loadList(system.file("list/NarcoticsDataset.csv",
package="RMassBankData"))
w <- msmsWorkflow(w, mode="pH", steps=c(1), archivename =
"pH_narcotics")
w <- newStep2WorkFlow(w, mode="pH", analyzeMethod="formula")
w <- msmsWorkflow(w, mode="pH", steps=c(3:4), archivename =
"pH_narcotics")
storedW <- loadMsmsWorkspace(system.file("results/pH_narcotics_RF.RData",
package="RMassBankData"))
storedW <- msmsWorkflow(storedW, mode="pH", steps=4)
w@rc <- storedW@rc
w@rc.ms1 <- storedW@rc.ms1
w <- msmsWorkflow(w, mode="pH", steps=4, archivename =
"pH_narcotics", newRecalibration = FALSE)
w <- msmsWorkflow(w, mode="pH", steps=c(5:8), archivename =
"pH_narcotics")
mb <- newMbWorkspace(w)
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists_incomplete",
package="RMassBankData"))
mb <- mbWorkflow(mb, infolist_path="./Narcotics_infolist.csv")
mb <- resetInfolists(mb)
mb <- loadInfolists(mb, system.file("infolists", package="RMassBankData"))
mb <- mbWorkflow(mb)
testSuite <- RUnit::defineTestSuite("Electronic noise and formula calculation Test", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.EN_FC.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testSuite2 <- RUnit::defineTestSuite("Evaluation of data acquisition process", dirs = system.file("unitTests",
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
rngNormalKind = "Kinderman-Ramage")
testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
file.remove(c("pH_narcotics_Failpeaks.csv","pH_narcotics.RData","pH_narcotics_RA.RData","pH_narcotics_RF.RData"))
RUnit::printTextProtocol(testData)
RUnit::printTextProtocol(testData2)
setwd(oldwd)
return(testData)
}
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