Mercurial > repos > pieterlukasse > prims_metabolomics2

## read args:
args <- commandArgs(TRUE)
## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
args.constructedDB <- args[1]
## data file in xset format:
args.xsetData <- args[2]
## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
args.settings <- args[3]

## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
args.outAnnotationTable <- args[4]

args.mass_error_function <- args[5]
if (args.mass_error_function == "0")
	args.mass_error_function <- NULL
## report files
args.htmlReportFile <- args[6]
args.htmlReportFile.files_path <- args[7]

if (length(args) == 8)
{
	args.outLogFile <- args[8]
	# suppress messages:
	# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
	msg <- file(args.outLogFile, open="wt")
	sink(msg, type="message")
	sink(msg, type="output")
}

cat("\nSettings used===============:\n")
cat(readChar(args.settings, 1e5))


tryCatch(
        {
	        library(metaMS)

			## load the constructed DB :
			tempEnv <- new.env()
			testDB <- load(args.constructedDB, envir=tempEnv)
			xsetData <- readRDS(args.xsetData)

			## load settings "script" into "customMetaMSsettings"
			source(args.settings, local=tempEnv)
			message(paste(" loaded : ", args.settings))

			# Just to highlight: if you want to use more than one
			# trigger runLC:
			LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, errf=args.mass_error_function, nSlaves=20, returnXset = TRUE)

			# write out runLC annotation results:
			write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)

			# the used constructed DB (write to log):
			cat("\nConstructed DB info===============:\n")
			str(tempEnv[[testDB[1]]]$Info)
			cat("\nConstructed DB table===============:\n")
			if (length(args) == 8)
			{
				write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
				write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
			}

			message("\nGenerating report.........")
			# report
			dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
			html <- "<html><body><h1>Summary of annotation results:</h1>"
			nrTotalFeatures <- nrow(LC$PeakTable)
			nrAnnotatedFeatures <- nrow(LC$Annotation$annotation.table)
			html <- paste(html,"<p>Total nr of features: ", nrTotalFeatures,"</p>", sep="")
			html <- paste(html,"<p>Total nr of annotated features: ", nrAnnotatedFeatures,"</p>", sep="")

			html <- paste(html,"</body><html>")
			message("finished generating report")
			write(html,file=args.htmlReportFile)
			# unlink(args.htmlReportFile)
			cat("\nWarnings================:\n")
			str( warnings() )
		},
        error=function(cond) {
            sink(NULL, type="message") # default setting
			sink(stderr(), type="output")
            message("\nERROR: ===========\n")
            print(cond)
        }
    )
author	linda-bakker
date	Fri, 24 Aug 2018 09:56:05 -0400
parents	4393f982d18f
children