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Merge pull request #277 from workflow4metabolomics/CAMERA_SUITE
Add camera new tools
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,173 @@ | ||
| #!/usr/bin/env Rscript | ||
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| # ----- PACKAGE ----- | ||
| cat("\tSESSION INFO\n") | ||
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| # Import the different functions | ||
| source_local <- function(fname) { | ||
| argv <- commandArgs(trailingOnly = FALSE) | ||
| base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | ||
| source(paste(base_dir, fname, sep = "/")) | ||
| } | ||
| source_local("lib.r") | ||
|
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| pkgs <- c("CAMERA", "xcms", "multtest", "batch") | ||
| loadAndDisplayPackages(pkgs) | ||
| cat("\n\n") | ||
| # ----- ARGUMENTS ----- | ||
| cat("\tARGUMENTS INFO\n") | ||
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| args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects | ||
| write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") | ||
|
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| cat("\n\n") | ||
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| print("Arguments retrieved from the command line:") | ||
| print(args) | ||
|
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| # Function to convert "NULL" strings to actual NULL values | ||
| convertNullString <- function(x) { | ||
| if (x == "NULL") { | ||
| return(NULL) | ||
| } | ||
| return(x) | ||
| } | ||
|
|
||
| # Function to convert string to numeric lists | ||
| convert_psg_list <- function(x) { | ||
| # Check if x is NULL or has zero length before further processing | ||
| if (is.null(x) || length(x) == 0) { | ||
| return(NULL) | ||
| } | ||
|
|
||
| # Force conversion to character | ||
| x <- as.character(x) | ||
|
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||
| if (grepl("^[0-9]+$", x)) { | ||
| # If the string represents a single numeric value | ||
| return(as.numeric(x)) | ||
| } else { | ||
| # Convert string representation of a list to a numeric vector | ||
| # Use a regular expression to split by common separators | ||
| return(as.numeric(unlist(strsplit(x, "[,;\\s]+")))) | ||
| } | ||
| } | ||
|
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| for (arg in names(args)) { | ||
| args[[arg]] <- convertNullString(args[[arg]]) | ||
| } | ||
|
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| # Convert only the 'psg_list' element in args | ||
| args$psg_list <- convert_psg_list(args$psg_list) | ||
|
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| print("Argument types:") | ||
| print(sapply(args, class)) | ||
|
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| # Check if the image file exists | ||
| if (!file.exists(args$image)) { | ||
| stop("The RData file does not exist: ", args$image) | ||
| } | ||
|
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| # ----- PROCESSING INFILE ----- | ||
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| # Load the RData file | ||
| load(args$image) | ||
| args$image <- NULL | ||
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| # Save arguments for report generation | ||
| if (!exists("listOFlistArguments")) listOFlistArguments <- list() | ||
| listOFlistArguments[[format(Sys.time(), "%y%m%d-%H:%M:%S_findAdducts")]] <- args | ||
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| # We unzip automatically the chromatograms from the zip files. | ||
| if (!exists("zipfile")) zipfile <- NULL | ||
| if (!exists("singlefile")) singlefile <- NULL | ||
| rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) | ||
| zipfile <- rawFilePath$zipfile | ||
| singlefile <- rawFilePath$singlefile | ||
| args <- rawFilePath$args | ||
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| print(paste("singlefile :", singlefile)) | ||
| if (!is.null(singlefile)) { | ||
| directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile) | ||
| } | ||
|
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| # Check if the 'rules' argument in 'args' is NULL | ||
| if (is.null(args$rules)) { | ||
| # If 'args$rules' is NULL, set 'rulset' to NULL | ||
| args$rulset <- NULL | ||
| } else { | ||
| # Try to read the rules file with different delimiters | ||
| delimiters <- c(";", "\t", ",") # List of possible delimiters | ||
| success <- FALSE # Flag to check if reading was successful | ||
|
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| for (sep in delimiters) { | ||
| # Attempt to read the rules file with the current separator | ||
| args$rulset <- read.table(args$rules, header = TRUE, sep = sep) | ||
|
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| # Check if the number of columns is at least 4 | ||
| if (ncol(args$rulset) >= 4) { | ||
| success <- TRUE # Mark success if the format is correct | ||
| break # Exit the loop if the file was read successfully | ||
| } | ||
| } | ||
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| # If reading the rules file failed for all delimiters | ||
| if (!success) { | ||
| # Display an error message if the file is not well formatted | ||
| error_message <- "The rules file appears to be improperly formatted. Accepted column separators are ;, tab, and ,." | ||
| print(error_message) | ||
| stop(error_message) # Stop execution with an error | ||
| } | ||
| } | ||
|
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| # Verify that the object xa is loaded | ||
| if (!exists("xa")) { | ||
| stop("The object xa was not found in the RData file.") | ||
| } | ||
|
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| print("Loaded xa object:") | ||
| print(xa) | ||
|
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| # Apply the findAdducts function on the xsAnnotate object | ||
| print("Calling findAdducts function:") | ||
| xa <- findAdducts(xa, ppm = args$ppm, mzabs = args$mzabs, multiplier = args$multiplier, polarity = args$polarity, rules = args$rulset, max_peaks = args$max_peaks, psg_list = args$psg_list, intval = args$intval) | ||
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| print("Result of findAdducts function:") | ||
| print(xa) | ||
|
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| # Extract the list of annotated peaks | ||
| peakList <- getPeaklist(xa, intval = args$intval) | ||
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| if (length(phenoData@data$sample_name) == 1) { | ||
| peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_") | ||
| variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))] | ||
| variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ) | ||
| } else { | ||
| names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals | ||
| names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals | ||
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| variableMetadata <- data.frame( | ||
| name = names_default, | ||
| name_custom = names_custom, | ||
| stringsAsFactors = FALSE | ||
| ) | ||
| variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]) | ||
| } | ||
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| if (!exists("RTinMinute")) RTinMinute <- FALSE | ||
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| if (args$convertRTMinute && RTinMinute == FALSE) { | ||
| RTinMinute <- TRUE | ||
| variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute) | ||
| } | ||
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| # Save the extracted peak list as a TSV file named 'variableMetadata.tsv' | ||
| output_file_tsv <- "variableMetadata.tsv" | ||
| write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE) | ||
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| # Save the updated xsAnnotate object | ||
| output_file_RData <- "camera_findAdducts.RData" | ||
| objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData") | ||
| save(list = objects2save[objects2save %in% ls()], file = output_file_RData) | ||
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| cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n") |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| #!/usr/bin/env Rscript | ||
|
|
||
| # ----- PACKAGE ----- | ||
| cat("\tSESSION INFO\n") | ||
|
|
||
| # Import the different functions | ||
| source_local <- function(fname) { | ||
| argv <- commandArgs(trailingOnly = FALSE) | ||
| base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | ||
| source(paste(base_dir, fname, sep = "/")) | ||
| } | ||
| source_local("lib.r") | ||
|
|
||
| pkgs <- c("CAMERA", "xcms", "multtest", "batch") | ||
| loadAndDisplayPackages(pkgs) | ||
| cat("\n\n") | ||
| # ----- ARGUMENTS ----- | ||
| cat("\tARGUMENTS INFO\n") | ||
|
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| args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects | ||
| write.table(as.matrix(args), col.names = FALSE, quote = FALSE, sep = "\t") | ||
|
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| cat("\n\n") | ||
|
|
||
| print("Arguments retrieved from the command line:") | ||
| print(args) | ||
|
|
||
| print("Argument types:") | ||
| print(sapply(args, class)) | ||
|
|
||
| # Check if the image file exists | ||
| if (!file.exists(args$image)) { | ||
| stop("The RData file does not exist: ", args$image) | ||
| } | ||
|
|
||
| # ----- PROCESSING INFILE ----- | ||
|
|
||
| # Load the RData file | ||
| load(args$image) | ||
| args$image <- NULL | ||
|
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||
| # Save arguments to generate a report | ||
| if (!exists("listOFlistArguments")) listOFlistArguments <- list() | ||
| listOFlistArguments[[format(Sys.time(), "%y%m%d-%H:%M:%S_findIsotopes")]] <- args | ||
|
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| # We unzip automatically the chromatograms from the zip files. | ||
| if (!exists("zipfile")) zipfile <- NULL | ||
| if (!exists("singlefile")) singlefile <- NULL | ||
| rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args) | ||
| zipfile <- rawFilePath$zipfile | ||
| singlefile <- rawFilePath$singlefile | ||
| args <- rawFilePath$args | ||
|
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| print(paste("singlefile :", singlefile)) | ||
| if (!is.null(singlefile)) { | ||
| directory <- retrieveRawfileInTheWorkingDir(singlefile, zipfile) | ||
| } | ||
|
|
||
| # Verify if the xa object is loaded | ||
| if (!exists("xa")) { | ||
| stop("The xa object was not found in the RData file.") | ||
| } | ||
|
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| print("xa object loaded:") | ||
| print(xa) | ||
|
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| print("calcIsotopeMatrix") | ||
| calcIsotopeMatrix <- function(maxiso = 4) { | ||
| if (!is.numeric(maxiso)) { | ||
| stop("Parameter maxiso is not numeric!\n") | ||
| } else if (maxiso < 1 || maxiso > 8) { | ||
| stop(paste( | ||
| "Parameter maxiso must be between 1 and 8. ", | ||
| "Otherwise, use your own IsotopeMatrix.\n" | ||
| ), sep = "") | ||
| } | ||
|
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| isotopeMatrix <- matrix(NA, 8, 4) | ||
| colnames(isotopeMatrix) <- c("mzmin", "mzmax", "intmin", "intmax") | ||
|
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| isotopeMatrix[1, ] <- c(1.000, 1.0040, 1.0, 150) | ||
| isotopeMatrix[2, ] <- c(0.997, 1.0040, 0.01, 200) | ||
| isotopeMatrix[3, ] <- c(1.000, 1.0040, 0.001, 200) | ||
| isotopeMatrix[4, ] <- c(1.000, 1.0040, 0.0001, 200) | ||
| isotopeMatrix[5, ] <- c(1.000, 1.0040, 0.00001, 200) | ||
| isotopeMatrix[6, ] <- c(1.000, 1.0040, 0.000001, 200) | ||
| isotopeMatrix[7, ] <- c(1.000, 1.0040, 0.0000001, 200) | ||
| isotopeMatrix[8, ] <- c(1.000, 1.0040, 0.00000001, 200) | ||
|
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| return(isotopeMatrix[1:maxiso, , drop = FALSE]) | ||
| } | ||
|
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| isotopeMatrix <- calcIsotopeMatrix(args$maxiso) | ||
|
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| # Apply the findIsotopes function on the xsAnnotate object | ||
| print("Calling findIsotopes function:") | ||
| xa <- findIsotopes(xa, maxcharge = args$maxcharge, maxiso = args$maxiso, ppm = args$ppm, mzabs = args$mzabs, intval = args$intval, minfrac = args$minfrac, isotopeMatrix = isotopeMatrix, filter = args$filter) | ||
|
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| print("Result of the findIsotopes function:") | ||
| print(xa) | ||
|
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| # Extract the list of annotated peaks | ||
| peakList <- getPeaklist(xa, intval = args$intval) | ||
|
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| if (length(phenoData@data$sample_name) == 1) { | ||
| peakList$name <- make.unique(paste0("M", round(peakList[, "mz"], 0), "T", round(peakList[, "rt"], 0)), "_") | ||
| variableMetadata <- peakList[, c("name", setdiff(names(peakList), "name"))] | ||
| variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ) | ||
| } else { | ||
| names_default <- groupnames(xa@xcmsSet, mzdec = 0, rtdec = 0) # Names without decimals | ||
| names_custom <- groupnames(xa@xcmsSet, mzdec = args$numDigitsMZ, rtdec = args$numDigitsRT) # Names with "x" decimals | ||
|
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| variableMetadata <- data.frame( | ||
| name = names_default, | ||
| name_custom = names_custom, | ||
| stringsAsFactors = FALSE | ||
| ) | ||
| variableMetadata <- cbind(variableMetadata, peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]) | ||
| } | ||
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| if (!exists("RTinMinute")) RTinMinute <- FALSE | ||
|
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| if (args$convertRTMinute && RTinMinute == FALSE) { | ||
| RTinMinute <- TRUE | ||
| variableMetadata <- RTSecondToMinute(variableMetadata = variableMetadata, convertRTMinute = args$convertRTMinute) | ||
| } | ||
|
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| # Saves the extracted peak list as a TSV file named 'variableMetadata.tsv' | ||
| output_file_tsv <- "variableMetadata.tsv" | ||
| write.table(variableMetadata, file = output_file_tsv, sep = "\t", row.names = FALSE, quote = FALSE) | ||
|
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| # Save the updated xsAnnotate object | ||
| output_file_RData <- "camera_findIsotopes.RData" | ||
|
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| objects2save <- c("xa", "variableMetadata", "listOFlistArguments", "zipfile", "singlefile", "RTinMinute", "phenoData") | ||
| save(list = objects2save[objects2save %in% ls()], file = output_file_RData) | ||
|
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| cat("Output files generated:", output_file_tsv, "and", output_file_RData, "\n") |
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