Mercurial > repos > pieterlukasse > prims_metabolomics

comparison 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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48:26b93438f30e 49:f772a5caa86a
1 ## read args:
2 args <- commandArgs(TRUE)
3 ## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
4 args.constructedDB <- args[1]
5 ## data file in xset format:
6 args.xsetData <- args[2]
7 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
8 args.settings <- args[3]
9
10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
11 args.outAnnotationTable <- args[4]
12
13 ## report files
14 args.htmlReportFile <- args[5]
15 args.htmlReportFile.files_path <- args[6]
16
17 if (length(args) == 7)
18 {
19 args.outLogFile <- args[7]
20 # suppress messages:
21 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
22 msg <- file(args.outLogFile, open="wt")
23 sink(msg, type="message")
24 sink(msg, type="output")
25 }
26
27 cat("\nSettings used===============:\n")
28 cat(readChar(args.settings, 1e5))
29
30
31 tryCatch(
32 {
33 library(metaMS)
34
35 ## load the constructed DB :
36 tempEnv <- new.env()
37 testDB <- load(args.constructedDB, envir=tempEnv)
38 xsetData <- readRDS(args.xsetData)
39
40 ## load settings "script" into "customMetaMSsettings"
41 source(args.settings, local=tempEnv)
42 message(paste(" loaded : ", args.settings))
43
44 # Just to highlight: if you want to use more than one
45 # trigger runLC:
46 LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
47
48 # write out runLC annotation results:
49 write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
50
51 # the used constructed DB (write to log):
52 cat("\nConstructed DB info===============:\n")
53 str(tempEnv[[testDB[1]]]$Info)
54 cat("\nConstructed DB table===============:\n")
55 if (length(args) == 7)
56 {
57 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
58 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
59 }
60
61 message("\nGenerating report.........")
62 # report
63 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
64 html <- "<html><body><h1>Summary of annotation results:</h1>"
65 nrTotalFeatures <- nrow(LC$PeakTable)
66 nrAnnotatedFeatures <- nrow(LC$Annotation$annotation.table)
67 html <- paste(html,"<p>Total nr of features: ", nrTotalFeatures,"</p>", sep="")
68 html <- paste(html,"<p>Total nr of annotated features: ", nrAnnotatedFeatures,"</p>", sep="")
69
70 html <- paste(html,"</body><html>")
71 message("finished generating report")
72 write(html,file=args.htmlReportFile)
73 # unlink(args.htmlReportFile)
74 cat("\nWarnings================:\n")
75 str( warnings() )
76 },
77 error=function(cond) {
78 sink(NULL, type="message") # default setting
79 sink(stderr(), type="output")
80 message("\nERROR: ===========\n")
81 print(cond)
82 }
83 )