ms2snoop: MS2snoop.R comparison

comparison MS2snoop.R @ 1:df2672c37732 draft

planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43

author	workflow4metabolomics
date	Tue, 24 May 2022 18:14:49 +0000
parents	91a3242fd67f
children	c68c94865667

comparison

equal deleted inserted replaced

-:91a3242fd67f
+:df2672c37732
 #' tested against data from other labs.
 #' new maintainer: Lain Pavot - lain.pavot@inrae.fr
 #'
 #' @import optparse
 #'
-NULL
+assign("MS2SNOOP_VERSION", "1.0.1")
+lockBinding("MS2SNOOP_VERSION", globalenv())
+assign("MISSING_PARAMETER_ERROR", 1)
+lockBinding("MISSING_PARAMETER_ERROR", globalenv())
+assign("BAD_PARAMETER_VALUE_ERROR", 2)
+lockBinding("BAD_PARAMETER_VALUE_ERROR", globalenv())
+assign("MISSING_INPUT_FILE_ERROR", 3)
+lockBinding("MISSING_INPUT_FILE_ERROR", globalenv())
+assign("NO_ANY_RESULT_ERROR", 255)
+lockBinding("NO_ANY_RESULT_ERROR", globalenv())
 assign("DEFAULT_PRECURSOR_PATH", "peaklist_precursors.tsv")
 assign("DEFAULT_FRAGMENTS_PATH", "peaklist_fragments.tsv")
 assign("DEFAULT_COMPOUNDS_PATH", "compounds_pos.txt")
 assign("DEFAULT_OUTPUT_PATH", "compound_fragments_result.txt")
 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", 60)
 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", globalenv())
 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", globalenv())
 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", globalenv())
 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", globalenv())
-debug <- FALSE
 ########################################################################
 #' @title plot_pseudo_spectra
 ## check if fragments corresponding to precursor are found in several
 ## files (collision energy)
 ## this lead to a processing for each fileid
 mf <- levels(as.factor(sprecini$fileid))
-if (length(mf) > 1) {
+if (length(mf) > 1 && global_verbose) {
 cat(" several files detected for this compounds :\n")
 }
 for (f in seq_along(mf)) {
 sfrgtfil <- data.frame(sfrgtfil, mznominal)
 ## creation of cross table row=scan col=mz X=ra
 vmz <- levels(as.factor(sfrgtfil$mznominal))
-cat(" fragments :", vmz)
+if (global_verbose) {
+cat(" fragments :", vmz)
+}
 ## mz of precursor in data precursor to check correlation with
 mz_prec <- paste0("mz", round(mean(sprec$mz), mzdecimal))
 for (m in seq_along(vmz)) {
 all.x = TRUE,
 all.y = TRUE
 )
 }
 }
-if (debug) {
+if (global_debug) {
+print(ds_abs_int)
 write.table(
 x = ds_abs_int,
 file = paste0(c_name, "ds_abs_int.txt"),
 row.names = FALSE,
 sep = "\t"
 cat(" non detected in fragments file \n")
 }
 if (!is.null(res_comp_by_file)) {
 res_comp <- rbind(res_comp, res_comp_by_file)
 }
-cat("\n")
+if (global_verbose) {
+cat("\n")
+}
 dev.off()
 }
 } else {
 res_comp <- NULL
 cat(" non detected in precursor file \n")
 }
 return(res_comp)
 }
+set_global <- function(var, value) {
+assign(var, value, envir = globalenv())
+}
+set_debug <- function() {
+set_global("global_debug", TRUE)
+}
+unset_debug <- function() {
+set_global("global_debug", FALSE)
+}
+set_verbose <- function() {
+set_global("global_verbose", TRUE)
+}
+unset_verbose <- function() {
+set_global("global_verbose", FALSE)
+}
 create_parser <- function() {
 parser <- optparse::OptionParser()
 parser <- optparse::add_option(
 parser,
 c("-v", "--verbose"),
 action = "store_true",
 default = FALSE,
-help = "Print extra output [default %default]"
+help = paste(
+"[default %default]",
+"Print extra output"
+)
+)
+parser <- optparse::add_option(
+parser,
+c("-V", "--version"),
+action = "store_true",
+default = FALSE,
+help = "Prints version and exits"
+)
+parser <- optparse::add_option(
+parser,
+c("-d", "--debug"),
+action = "store_true",
+default = FALSE,
+help = paste(
+"[default %default]",
+"Print debug outputs"
+)
 )
 parser <- optparse::add_option(
 parser,
 c("-o", "--output"),
 type = "character",
 parser,
 c("--tolmz"),
 type = "numeric",
 action = "store",
 default = DEFAULT_TOLMZ,
-metavar = "number"
+metavar = "number",
+help = paste(
+"[default %default]",
+"Tolerance for MZ (in Dalton) to match the standard in the compounds"
+)
 )
 parser <- optparse::add_option(
 parser,
 c("--tolrt"),
 type = "integer",
 action = "store",
 default = DEFAULT_TOLRT,
-metavar = "number"
+metavar = "number",
+help = paste(
+"[default %default]",
+"RT (in seconds) to match the standard in the compounds"
+)
 )
 parser <- optparse::add_option(
 parser,
 c("--seuil_ra"),
 type = "numeric",
 action = "store",
-help = "relative intensity threshold",
 default = DEFAULT_SEUIL_RA,
-metavar = "number"
+metavar = "number",
+help = paste(
+"[default %default]",
+"relative intensity threshold"
+),
 )
 parser <- optparse::add_option(
 parser,
 c("--mzdecimal"),
 type = "integer",
 default = DEFAULT_MZDECIMAL,
 action = "store",
-help = "nb decimal for mz",
+help = paste(
+"[default %default]",
+"Number of decimal to write for MZ"
+),
 metavar = "number"
 )
 parser <- optparse::add_option(
 parser,
 c("--r_threshold"),
 type = "integer",
 default = DEFAULT_R_THRESHOLD,
 action = "store",
-help = paste0(
+help = paste(
-"r pearson correlation threshold between precursor and fragment ",
+"[default %default]",
+"R-Pearson correlation threshold between precursor and fragment",
 "absolute intensity"
 ),
 metavar = "number"
 )
 parser <- optparse::add_option(
 parser,
 c("--min_number_scan"),
 type = "numeric",
 action = "store",
 default = DEFAULT_MINNUMBERSCAN,
-help = paste0(
+help = paste(
-"fragments are kept if there are found in a minimum number ",
+"[default %default]",
-"of scans"
+"Fragments are kept if there are found in a minimum number",
+"of min_number_scan scans"
 ),
 metavar = "number"
 )
 return(parser)
 }
+stop_with_status <- function(msg, status) {
+message(sprintf("Error: %s", msg))
+message(sprintf("Error code: %s", status))
+base::quit(status = status)
+}
+check_args_validity <- function(args) { ## nolint cyclocomp_linter
+sysvars <- Sys.getenv()
+sysvarnames <- names(sysvars)
+if (length(args$output) == 0 || nchar(args$output[1]) == 0) {
+stop_with_status(
+"Missing output parameters. Please set it with --output.",
+MISSING_PARAMETER_ERROR
+)
+}
+if (length(args$precursors) == 0 || nchar(args$precursors[1]) == 0) {
+stop_with_status(
+"Missing precursors parameters. Please set it with --precursors.",
+MISSING_PARAMETER_ERROR
+)
+}
+if (length(args$fragments) == 0 || nchar(args$fragments[1]) == 0) {
+stop_with_status(
+"Missing fragments parameters. Please set it with --fragments.",
+MISSING_PARAMETER_ERROR
+)
+}
+if (length(args$compounds) == 0 || nchar(args$compounds[1]) == 0) {
+stop_with_status(
+"Missing compounds parameters. Please set it with --compounds.",
+MISSING_PARAMETER_ERROR
+)
+}
+if (!file.exists(args$precursors)) {
+stop_with_status(
+sprintf(
+"Precursors file %s does not exist or cannot be accessed.",
+args$precursors
+),
+MISSING_INPUT_FILE_ERROR
+)
+}
+if (!file.exists(args$fragments)) {
+stop_with_status(
+sprintf(
+"Fragments file %s does not exist or cannot be accessed.",
+args$fragments
+),
+MISSING_INPUT_FILE_ERROR
+)
+}
+if (!file.exists(args$compounds)) {
+stop_with_status(
+sprintf(
+"Compounds file %s does not exist or cannot be accessed.",
+args$compounds
+),
+MISSING_INPUT_FILE_ERROR
+)
+}
+if (
+"_GALAXY_JOB_HOME_DIR" %in% sysvarnames
+|| "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
+|| "GALAXY_MEMORY_MB" %in% sysvarnames
+|| "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
+|| "GALAXY_SLOTS" %in% sysvarnames
+) {
+check_galaxy_args_validity(args)
+}
+}
+check_galaxy_args_validity <- function(args) {
+if (!file.exists(args$output)) {
+stop_with_status(
+sprintf(
+"Output file %s does not exist or cannot be accessed.",
+args$output
+),
+MISSING_INPUT_FILE_ERROR
+)
+}
+}
 main <- function(args) {
-## FOLDER AND FILES
+if (args$version) {
+cat(sprintf("%s\n", MS2SNOOP_VERSION))
+base::quit(status = 0)
+}
+sessionInfo()
+check_args_validity(args)
+if (args$debug) {
+set_debug()
+}
+if (args$verbose) {
+set_verbose()
+}
 ## MSpurity precursors file
 precursors <- read.table(
 file = args$precursors,
 header = TRUE,
 sep = "\t",
 file = args$compounds,
 sep = "\t",
 quote = "\"",
 header = TRUE
 )
-## PARAMETERS
-## tolerance for mz(dalton) rt(seconds) to match the standard in the compounds
+res_all <- NULL
-## list with the precursor MSpurity file
-tolmz <- args$tolmz
-tolrt <- args$tolrt
-##  relative intensity threshold
-seuil_ra <- args$seuil_ra
-## nb decimal for mz
-mzdecimal <- args$mzdecimal
-## r pearson correlation threshold between precursor and
-# #fragment absolute intensity
-r_threshold <- args$r_threshold
-## fragments are kept if there are found in a minimum number of scans
-min_number_scan <- args$min_number_scan
 for (i in seq_len(nrow(compounds))) {
 ## loop execution for all compounds in the compounds file
 res_cor <- NULL
 res_cor <- extract_fragments(
 precursors = precursors,
 fragments = fragments,
 mzref = compounds[[2]][i],
 rtref = compounds[[3]][i],
 c_name = compounds[[1]][i],
-min_number_scan = min_number_scan,
+min_number_scan = args$min_number_scan,
-mzdecimal = mzdecimal,
+mzdecimal = args$mzdecimal,
-r_threshold = r_threshold,
+r_threshold = args$r_threshold,
-seuil_ra = seuil_ra,
+seuil_ra = args$seuil_ra,
-tolmz = tolmz,
+tolmz = args$tolmz,
-tolrt = tolrt
+tolrt = args$tolrt
 )
-if (i == 1 & !is.null(res_cor)) {
+if (!is.null(res_cor)) {
-res_all <- res_cor
+if (is.null(res_all)) {
-} else if (!is.null(res_cor)) {
+res_all <- res_cor
-res_all <- rbind(res_all, res_cor)
+} else {
+res_all <- rbind(res_all, res_cor)
+}
 }
 }
 if (is.null(res_all)) {
-stop("No result at all!")
+stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
 }
 write.table(
 x = res_all,
 file = args$output,
 sep = "\t",
 row.names = FALSE
 )
 }
+unset_debug()
+unset_verbose()
 args <- optparse::parse_args(create_parser())
-sessionInfo()
 main(args)
 warnings()

Mercurial > repos > workflow4metabolomics > ms2snoop

comparison MS2snoop.R @ 1:df2672c37732 draft