Mercurial > repos > lecorguille > mnsbase_readmsdata

annotate msnbase_readmsdata.r @ 0:3f0a218e2ebc draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:45:58 -0400
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3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
lecorguille
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1 #!/usr/bin/env Rscript
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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3 # ----- LOG FILE -----
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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4 log_file <- file("log.txt", open="wt")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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5 sink(log_file)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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6 sink(log_file, type = "output")
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9 # ----- PACKAGE -----
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10 cat("\tSESSION INFO\n")
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12 #Import the different functions
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) }
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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14 source_local("lib.r")
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16 pkgs <- c("MSnbase","batch")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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17 loadAndDisplayPackages(pkgs)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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18 cat("\n\n");
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21 # ----- ARGUMENTS -----
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22 cat("\tARGUMENTS INFO\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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23 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects
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24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t')
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26 cat("\n\n")
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29 # ----- PROCESSING INFILE -----
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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30 cat("\tARGUMENTS PROCESSING INFO\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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33 cat("\n\n")
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35 # ----- INFILE PROCESSING -----
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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36 cat("\tINFILE PROCESSING INFO\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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38 # Handle infiles
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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39 if (!exists("singlefile")) singlefile <- NULL
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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40 if (!exists("zipfile")) zipfile <- NULL
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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41 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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42 zipfile <- rawFilePath$zipfile
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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43 singlefile <- rawFilePath$singlefile
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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44 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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46 # Check some character issues
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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47 md5sumList <- list("origin" = getMd5sum(directory))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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48 checkXmlStructure(directory)
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49 checkFilesCompatibilityWithXcms(directory)
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52 cat("\n\n")
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55 # ----- MAIN PROCESSING INFO -----
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56 cat("\tMAIN PROCESSING INFO\n")
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59 cat("\t\tCOMPUTE\n")
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61 ## Get the full path to the files
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62 files <- getMSFiles(directory)
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64 cat("\t\t\tCreate a phenodata data.frame\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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65 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1))
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66 s_name <- tools::file_path_sans_ext(basename(files))
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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67 pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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68 print(pd)
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70 cat("\t\t\tLoad Raw Data\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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71 raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk")
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73 # Transform the files absolute pathways into relative pathways
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74 raw_data@processingData@files <- sub(paste(getwd(), "/", sep="") , "", raw_data@processingData@files)
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76 # Create a sampleMetada file
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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77 sampleNamesList <- getSampleMetadata(xdata=raw_data, sampleMetadataOutput="sampleMetadata.tsv")
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79 cat("\n\n")
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81 # ----- EXPORT -----
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83 cat("\tMSnExp OBJECT INFO\n")
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84 print(raw_data)
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85 cat("\t\tphenoData\n")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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86 print(raw_data@phenoData@data)
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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87 cat("\n\n")
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89 #saving R data in .Rdata file to save the variables used in the present tool
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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90 objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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91 save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData")
3f0a218e2ebc planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
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94 cat("\tDONE\n")