Mercurial > repos > pieterlukasse > prims_metabolomics

annotate metaMS_cmd_annotate.r @ 52:5b1adc49700d

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small adjustment
author pieter.lukasse@wur.nl
date Thu, 11 Dec 2014 10:26:17 +0100
parents f772a5caa86a
children 70574a6381ea
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49
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1 ## read args:
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2 args <- commandArgs(TRUE)
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3 ## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
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4 args.constructedDB <- args[1]
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5 ## data file in xset format:
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6 args.xsetData <- args[2]
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7 ## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
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8 args.settings <- args[3]
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9
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10 ## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
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11 args.outAnnotationTable <- args[4]
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12
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13 ## report files
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14 args.htmlReportFile <- args[5]
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15 args.htmlReportFile.files_path <- args[6]
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16
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17 if (length(args) == 7)
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18 {
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19 args.outLogFile <- args[7]
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20 # suppress messages:
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21 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
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22 msg <- file(args.outLogFile, open="wt")
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23 sink(msg, type="message")
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24 sink(msg, type="output")
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25 }
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26
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27 cat("\nSettings used===============:\n")
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28 cat(readChar(args.settings, 1e5))
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29
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30
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31 tryCatch(
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32 {
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33 library(metaMS)
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34
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35 ## load the constructed DB :
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36 tempEnv <- new.env()
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37 testDB <- load(args.constructedDB, envir=tempEnv)
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38 xsetData <- readRDS(args.xsetData)
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39
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40 ## load settings "script" into "customMetaMSsettings"
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41 source(args.settings, local=tempEnv)
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42 message(paste(" loaded : ", args.settings))
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43
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44 # Just to highlight: if you want to use more than one
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45 # trigger runLC:
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46 LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
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47
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48 # write out runLC annotation results:
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49 write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
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50
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51 # the used constructed DB (write to log):
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52 cat("\nConstructed DB info===============:\n")
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53 str(tempEnv[[testDB[1]]]$Info)
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54 cat("\nConstructed DB table===============:\n")
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55 if (length(args) == 7)
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56 {
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57 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
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58 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
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59 }
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60
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61 message("\nGenerating report.........")
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62 # report
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63 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
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64 html <- "<html><body><h1>Summary of annotation results:</h1>"
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65 nrTotalFeatures <- nrow(LC$PeakTable)
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66 nrAnnotatedFeatures <- nrow(LC$Annotation$annotation.table)
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67 html <- paste(html,"<p>Total nr of features: ", nrTotalFeatures,"</p>", sep="")
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68 html <- paste(html,"<p>Total nr of annotated features: ", nrAnnotatedFeatures,"</p>", sep="")
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69
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70 html <- paste(html,"</body><html>")
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71 message("finished generating report")
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72 write(html,file=args.htmlReportFile)
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73 # unlink(args.htmlReportFile)
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74 cat("\nWarnings================:\n")
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75 str( warnings() )
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76 },
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77 error=function(cond) {
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78 sink(NULL, type="message") # default setting
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79 sink(stderr(), type="output")
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80 message("\nERROR: ===========\n")
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81 print(cond)
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82 }
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83 )