Mercurial > repos > pieterlukasse > prims_metabolomics

diff metaMS_cmd_annotate.r @ 49:f772a5caa86a

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Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
parents
children 70574a6381ea
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS_cmd_annotate.r	Wed Dec 10 22:03:27 2014 +0100
@@ -0,0 +1,83 @@
+## 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]
+
+## report files
+args.htmlReportFile <- args[5]
+args.htmlReportFile.files_path <- args[6]
+
+if (length(args) == 7)
+{
+	args.outLogFile <- args[7]
+	# 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]]]$DB, nSlaves=20, returnXset = TRUE)
+			
+			# write out runLC annotation results:
+			write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
+			
+			# the used constructed DB (write to log):
+			cat("\nConstructed DB info===============:\n")
+			str(tempEnv[[testDB[1]]]$Info)
+			cat("\nConstructed DB table===============:\n") 
+			if (length(args) == 7)
+			{
+				write.table(tempEnv[[testDB[1]]]$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)
+        }
+    )