diff --git a/R/RmbWorkspace.R b/R/RmbWorkspace.R
index 72fe617694a07f84de73916f8f8b5eb99079b635..05b01d2ff9127a1a76239c6d78d8105d68caac3a 100755
--- a/R/RmbWorkspace.R
+++ b/R/RmbWorkspace.R
@@ -144,7 +144,9 @@ setClass("mbWorkspace",
# output data:
compiled = "list",
compiled_ok = "list",
+ compiled_notOk = "list",
mbfiles = "list",
+ mbfiles_notOk = "list",
molfile = "list",
ok = "integer",
problems = "integer"
diff --git a/R/createMassBank.R b/R/createMassBank.R
index 872bcb73f664d82c2df6157ea6f79b10bc9ddbac..50d23f6f303e973876e832fb2edfc821cd9cb4ed 100755
--- a/R/createMassBank.R
+++ b/R/createMassBank.R
@@ -75,26 +75,32 @@ loadInfolist <- function(mb, fileName)
"COMMENT.ID"
# Clear from padding spaces and NAs
- mbdata_new <- as.data.frame(t(apply(mbdata_new, 1, function(r)
+ mbdata_new <- as.data.frame(x = t(apply(mbdata_new, 1, function(r)
{
# Substitute empty spaces by real NA values
r[which(r == "")] <- NA
# Trim spaces (in all non-NA fields)
r[which(!is.na(r))] <- sub("^ *([^ ]+) *$", "\\1", r[which(!is.na(r))])
return(r)
- })))
+ })), stringsAsFactors = FALSE)
# use only the columns present in mbdata_archive, no other columns added in excel
mbdata_new <- mbdata_new[, colnames(mb@mbdata_archive)]
# substitute the old entires with the ones from our files
# then find the new (previously inexistent) entries, and rbind them to the table
new_entries <- setdiff(mbdata_new$id, mb@mbdata_archive$id)
old_entries <- intersect(mbdata_new$id, mb@mbdata_archive$id)
+
+ for(colname in colnames(mb@mbdata_archive))
+ mb@mbdata_archive[, colname] <- as.character(mb@mbdata_archive[, colname])
+
for(entry in old_entries)
mb@mbdata_archive[mb@mbdata_archive$id == entry,] <- mbdata_new[mbdata_new$id == entry,]
- mb@mbdata_archive <- rbind(mb@mbdata_archive,
- mbdata_new[mbdata_new$id==new_entries,])
+ mb@mbdata_archive <- rbind(mb@mbdata_archive, mbdata_new[mbdata_new$id==new_entries,])
+
+ for(colname in colnames(mb@mbdata_archive))
+ mb@mbdata_archive[, colname] <- as.factor(mb@mbdata_archive[, colname])
+
return(mb)
-
}
@@ -229,9 +235,7 @@ mbWorkflow <- function(mb, steps=c(1,2,3,4,5,6,7,8), infolist_path="./infolist.c
if(4 %in% steps)
{
message("mbWorkflow: Step 4. Spectra compilation")
- mb@compiled <- lapply(
- selectSpectra(mb@spectra, "found", "object"),
- function(r) {
+ mb@compiled <- lapply(X = selectSpectra(mb@spectra, "found", "object"), FUN = function(r) {
message(paste("Compiling: ", r@name, sep=""))
mbdata <- mb@mbdata_relisted[[which(mb@mbdata_archive$id == as.numeric(r@id))]]
if(nrow(mb@additionalPeaks) > 0)
@@ -241,41 +245,86 @@ mbWorkflow <- function(mb, steps=c(1,2,3,4,5,6,7,8), infolist_path="./infolist.c
return(res)
})
# check which compounds have useful spectra
- mb@ok <- which(!is.na(mb@compiled) & !(lapply(mb@compiled, length)==0))
+ ok <- unlist(lapply(X = selectSpectra(mb@spectra, "found", "object"), FUN = function(spec){unlist(lapply(X = spec@children, FUN = function(child){child@ok}))}))
+ mb@ok <- which(ok)
+ #mb@ok <- which(!is.na(mb@compiled) & !(lapply(mb@compiled, length)==0))
mb@problems <- which(is.na(mb@compiled))
- mb@compiled_ok <- mb@compiled[mb@ok]
+ mb@compiled_ok <- mb@compiled[mb@ok]
+ mb@compiled_notOk <- mb@compiled[!ok]
}
# Step 5: Convert the internal tree-like representation of the MassBank data into
# flat-text string arrays (basically, into text-file style, but still in memory)
if(5 %in% steps)
{
message("mbWorkflow: Step 5. Flattening records")
- mb@mbfiles <- lapply(mb@compiled_ok, function(c) lapply(c, toMassbank))
+ mb@mbfiles <- lapply(mb@compiled_ok, function(c) lapply(c, toMassbank))
+ mb@mbfiles_notOk <- lapply(mb@compiled_notOk, function(c) lapply(c, toMassbank))
}
# Step 6: For all OK records, generate a corresponding molfile with the structure
# of the compound, based on the SMILES entry from the MassBank record. (This molfile
# is still in memory only, not yet a physical file)
if(6 %in% steps)
{
- message("mbWorkflow: Step 6. Generate molfiles")
- mb@molfile <- lapply(mb@compiled_ok, function(c) createMolfile(as.numeric(c[[1]][['COMMENT']][[getOption("RMassBank")$annotations$internal_id_fieldname]])))
+ if(RMassBank.env$export.molfiles){
+ message("mbWorkflow: Step 6. Generate molfiles")
+ mb@molfile <- lapply(mb@compiled_ok, function(c) createMolfile(as.numeric(c[[1]][['COMMENT']][[getOption("RMassBank")$annotations$internal_id_fieldname]])))
+ } else
+ warning("RMassBank is configured not to export molfiles (RMassBank.env$export.molfiles). Step 6 is therefore ignored.")
}
# Step 7: If necessary, generate the appropriate subdirectories, and actually write
# the files to disk.
if(7 %in% steps)
{
message("mbWorkflow: Step 7. Generate subdirs and export")
- dir.create(paste(getOption("RMassBank")$annotations$entry_prefix, "moldata", sep='/'),recursive=TRUE)
- dir.create(paste(getOption("RMassBank")$annotations$entry_prefix, "recdata", sep='/'),recursive=TRUE)
- for(cnt in seq_along(mb@compiled_ok))
- exportMassbank(mb@compiled_ok[[cnt]], mb@mbfiles[[cnt]], mb@molfile[[cnt]])
+
+ ## create folder
+ filePath_recData_valid <- file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata")
+ filePath_recData_invalid <- file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata_invalid")
+ filePath_molData <- file.path(getOption("RMassBank")$annotations$entry_prefix, "moldata")
+
+ dir.create(filePath_recData_valid,recursive=TRUE)
+ if(RMassBank.env$export.molfiles)
+ dir.create(filePath_molData,recursive=TRUE)
+ if(RMassBank.env$export.invalid)
+ dir.create(filePath_recData_invalid,recursive=TRUE)
+
+ if(length(mb@molfile) == 0)
+ mb@molfile <- as.list(rep(x = NA, times = length(mb@compiled_ok)))
+
+ ## export valid spectra
+ for(cnt in seq_along(mb@compiled_ok)){
+ exportMassbank_recdata(
+ accessions = unlist(lapply(X = mb@compiled_ok[[cnt]], FUN = "[", "ACCESSION")),
+ files = mb@mbfiles[[cnt]],
+ recDataFolder = filePath_recData_valid
+ )
+
+ if(findLevel(mb@compiled_ok[[cnt]][[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]][[1]],TRUE)=="standard" & RMassBank.env$export.molfiles)
+ exportMassbank_moldata(
+ cpdID = as.numeric(mb@compiled_ok[[cnt]][[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]][[1]]),
+ molfile = mb@molfile[[cnt]],
+ molDataFolder = filePath_molData
+ )
+ }
+
+ ## export invalid spectra
+ if(RMassBank.env$export.invalid)
+ for(cnt in seq_along(mb@compiled_notOk))
+ exportMassbank_recdata(
+ accessions = unlist(lapply(X = mb@compiled_notOk[[cnt]], FUN = "[", "ACCESSION")),
+ files = mb@mbfiles_notOk[[cnt]],
+ recDataFolder = filePath_recData_invalid
+ )
}
# Step 8: Create the list.tsv in the molfiles folder, which is required by MassBank
# to attribute substances to their corresponding structure molfiles.
if(8 %in% steps)
{
- message("mbWorkflow: Step 8. Create list.tsv")
- makeMollist(mb@compiled_ok)
+ if(RMassBank.env$export.molfiles){
+ message("mbWorkflow: Step 8. Create list.tsv")
+ makeMollist(compiled = mb@compiled_ok)
+ } else
+ warning("RMassBank is configured not to export molfiles (RMassBank.env$export.molfiles). Step 8 is therefore ignored.")
}
return(mb)
}
@@ -1289,20 +1338,21 @@ gatherSpectrum <- function(spec, msmsdata, ac_ms, ac_lc, aggregated, additionalP
{
# If the spectrum is not filled, return right now. All "NA" spectra will
# not be treated further.
- if(msmsdata@ok == FALSE)
+ if(msmsdata@ok == FALSE & !RMassBank.env$export.invalid)
return(NA)
# get data
scan <- msmsdata@acquisitionNum
id <- spec@id
# Further fill the ac_ms datasets, and add the ms$focused_ion with spectrum-specific data:
precursor_types <- list(
- "pH" = "[M+H]+",
- "pNa" = "[M+Na]+",
- "mH" = "[M-H]-",
- "mFA" = "[M+HCOO-]-",
- "pM" = "[M]+",
- "mM" = "[M]-",
- "pNH4" = "[M+NH4]+")
+ "pH" = "[M+H]+",
+ "pNa" = "[M+Na]+",
+ "mH" = "[M-H]-",
+ "mFA" = "[M+HCOO-]-",
+ "pM" = "[M]+",
+ "mM" = "[M]-",
+ "pNH4" = "[M+NH4]+"
+ )
ac_ms[['FRAGMENTATION_MODE']] <- msmsdata@info$mode
#ac_ms['PRECURSOR_TYPE'] <- precursor_types[spec$mode]
ac_ms[['COLLISION_ENERGY']] <- msmsdata@info$ce
@@ -1902,28 +1952,35 @@ toMassbank <- function (mbdata)
#' }
#'
#' @export
-exportMassbank <- function(compiled, files, molfile)
+exportMassbank <- function(compiled, files, molfile){
+ exportMassbank_recdata(
+ accessions = unlist(lapply(X = compiled, FUN = "[", "ACCESSION")),
+ files,
+ recDataFolder = file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata")
+ )
+ exportMassbank_moldata(
+ cpdID = as.numeric(compiled[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]][[1]]),
+ molfile,
+ molDataFolder = file.path(getOption("RMassBank")$annotations$entry_prefix, "moldata")
+ )
+}
+
+exportMassbank_recdata <- function(accessions, files, recDataFolder)
{
- molnames <- c()
- for(file in 1:length(compiled))
+ for(fileIdx in 1:length(accessions))
{
- # Read the accession no. from the corresponding "compiled" entry
- filename <- compiled[[file]]["ACCESSION"]
# use this accession no. as filename
- filename <- paste(filename, ".txt", sep="")
- write(files[[file]],
- file.path(getOption("RMassBank")$annotations$entry_prefix, "recdata",filename)
- )
+ filename <- paste(accessions[[fileIdx]], ".txt", sep="")
+ filePath <- file.path(recDataFolder,filename)
+ write(files[[fileIdx]], filePath)
}
+}
+exportMassbank_moldata <- function(cpdID, molfile, molDataFolder)
+{
# Use internal ID for naming the molfiles
- if(findLevel(compiled[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]][[1]],TRUE)=="standard"){
- molname <- sprintf("%04d", as.numeric(
- compiled[[1]][["COMMENT"]][[getOption("RMassBank")$annotations$internal_id_fieldname]][[1]]))
- molname <- paste(molname, ".mol", sep="")
- write(molfile,
- file.path(getOption("RMassBank")$annotations$entry_prefix, "moldata",molname)
- )
- }
+ molname <- sprintf("%04d", cpdID)
+ molname <- paste(molname, ".mol", sep="")
+ write(molfile,file.path(molDataFolder,molname))
}
# Makes a list.tsv with molfile -> massbank ch$name attribution.
diff --git a/R/zzz.R b/R/zzz.R
index 3a53d8c920bcaa7ee6eb46cf3a9b560b9b88d456..b43f08a598e414aef875a5a4f797c79589fd0e0c 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -2,7 +2,10 @@
RMassBank.env <<- new.env()
RMassBank.env$ReadAnnotation <- FALSE
RMassBank.env$testnumber <- 1
- RMassBank.env$verbose.output <- TRUE
+ ## new variables
+ RMassBank.env$verbose.output <- FALSE
+ RMassBank.env$export.invalid <- FALSE
+ RMassBank.env$export.molfiles <- TRUE
mb <- list()
attach(RMassBank.env)