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6
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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 args.mass_error_function <- args[5]
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14 if (args.mass_error_function == "0")
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15 args.mass_error_function <- NULL
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16 ## report files
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17 args.htmlReportFile <- args[6]
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18 args.htmlReportFile.files_path <- args[7]
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19
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20 if (length(args) == 8)
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21 {
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22 args.outLogFile <- args[8]
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23 # suppress messages:
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24 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
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25 msg <- file(args.outLogFile, open="wt")
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26 sink(msg, type="message")
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27 sink(msg, type="output")
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28 }
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29
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30 cat("\nSettings used===============:\n")
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31 cat(readChar(args.settings, 1e5))
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32
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33
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34 tryCatch(
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35 {
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36 library(metaMS)
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37
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38 ## load the constructed DB :
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39 tempEnv <- new.env()
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40 testDB <- load(args.constructedDB, envir=tempEnv)
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41 xsetData <- readRDS(args.xsetData)
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42
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43 ## load settings "script" into "customMetaMSsettings"
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44 source(args.settings, local=tempEnv)
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45 message(paste(" loaded : ", args.settings))
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46
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47 # Just to highlight: if you want to use more than one
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48 # trigger runLC:
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49 LC <- runLC(xset=xsetData, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, errf=args.mass_error_function, nSlaves=20, returnXset = TRUE)
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50
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51 # write out runLC annotation results:
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52 write.table(LC$PeakTable, args.outAnnotationTable, sep="\t", row.names=FALSE)
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53
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54 # the used constructed DB (write to log):
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55 cat("\nConstructed DB info===============:\n")
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56 str(tempEnv[[testDB[1]]]$Info)
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57 cat("\nConstructed DB table===============:\n")
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58 if (length(args) == 8)
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59 {
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60 write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
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61 write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
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62 }
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63
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64 message("\nGenerating report.........")
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65 # report
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66 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
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67 html <- "<html><body><h1>Summary of annotation results:</h1>"
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68 nrTotalFeatures <- nrow(LC$PeakTable)
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69 nrAnnotatedFeatures <- nrow(LC$Annotation$annotation.table)
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70 html <- paste(html,"<p>Total nr of features: ", nrTotalFeatures,"</p>", sep="")
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71 html <- paste(html,"<p>Total nr of annotated features: ", nrAnnotatedFeatures,"</p>", sep="")
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72
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73 html <- paste(html,"</body><html>")
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74 message("finished generating report")
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75 write(html,file=args.htmlReportFile)
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76 # unlink(args.htmlReportFile)
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77 cat("\nWarnings================:\n")
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78 str( warnings() )
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79 },
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80 error=function(cond) {
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81 sink(NULL, type="message") # default setting
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82 sink(stderr(), type="output")
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83 message("\nERROR: ===========\n")
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84 print(cond)
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85 }
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86 )
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