Mercurial > repos > lecorguille > msnbase_readmsdata
comparison msnbase_readmsdata.r @ 14:11ab2081bd4a draft
"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit dff3ac53c7c305ff263e6358308db48cf9ed4e27"
author | workflow4metabolomics |
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date | Mon, 12 Apr 2021 09:35:02 +0000 |
parents | 226fb89cacc4 |
children | 7faf9b2d83f6 |
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13:226fb89cacc4 | 14:11ab2081bd4a |
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1 #!/usr/bin/env Rscript | 1 #!/usr/bin/env Rscript |
2 | 2 |
3 # ----- LOG FILE ----- | 3 # ----- LOG FILE ----- |
4 log_file <- file("log.txt", open="wt") | 4 log_file <- file("log.txt", open = "wt") |
5 sink(log_file) | 5 sink(log_file) |
6 sink(log_file, type = "output") | 6 sink(log_file, type = "output") |
7 | 7 |
8 | 8 |
9 # ----- PACKAGE ----- | 9 # ----- PACKAGE ----- |
10 cat("\tSESSION INFO\n") | 10 cat("\tSESSION INFO\n") |
11 | 11 |
12 #Import the different functions | 12 #Import the different functions |
13 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } | 13 source_local <- function(fname) { |
14 argv <- commandArgs(trailingOnly = FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep = "/")) | |
15 } | |
14 source_local("lib.r") | 16 source_local("lib.r") |
15 | 17 |
16 pkgs <- c("MSnbase","batch") | 18 pkgs <- c("MSnbase", "batch") |
17 loadAndDisplayPackages(pkgs) | 19 loadAndDisplayPackages(pkgs) |
18 cat("\n\n"); | 20 cat("\n\n"); |
19 | 21 |
20 | 22 |
21 # ----- ARGUMENTS ----- | 23 # ----- ARGUMENTS ----- |
22 cat("\tARGUMENTS INFO\n") | 24 cat("\tARGUMENTS INFO\n") |
23 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects | 25 args <- parseCommandArgs(evaluate = FALSE) #interpretation of arguments given in command line as an R list of objects |
24 write.table(as.matrix(args), col.names=F, quote=F, sep='\t') | 26 write.table(as.matrix(args), col.names = F, quote = F, sep = "\t") |
25 | 27 |
26 cat("\n\n") | 28 cat("\n\n") |
27 | 29 |
28 | 30 |
29 # ----- PROCESSING INFILE ----- | 31 # ----- PROCESSING INFILE ----- |
36 cat("\tINFILE PROCESSING INFO\n") | 38 cat("\tINFILE PROCESSING INFO\n") |
37 | 39 |
38 # Handle infiles | 40 # Handle infiles |
39 if (!exists("singlefile")) singlefile <- NULL | 41 if (!exists("singlefile")) singlefile <- NULL |
40 if (!exists("zipfile")) zipfile <- NULL | 42 if (!exists("zipfile")) zipfile <- NULL |
41 rawFilePath <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile, args) | 43 rawFilePath <- retrieveRawfileInTheWorkingDir(singlefile, zipfile, args) |
42 zipfile <- rawFilePath$zipfile | 44 zipfile <- rawFilePath$zipfile |
43 singlefile <- rawFilePath$singlefile | 45 singlefile <- rawFilePath$singlefile |
44 files <- rawFilePath$files | 46 files <- rawFilePath$files |
45 | 47 |
46 md5sumList <- list("origin" = getMd5sum(files)) | 48 md5sumList <- list("origin" = getMd5sum(files)) |
53 | 55 |
54 | 56 |
55 cat("\t\tCOMPUTE\n") | 57 cat("\t\tCOMPUTE\n") |
56 | 58 |
57 cat("\t\t\tCreate a phenodata data.frame\n") | 59 cat("\t\t\tCreate a phenodata data.frame\n") |
58 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x),"/")), n=1)) | 60 s_groups <- sapply(files, function(x) tail(unlist(strsplit(dirname(x), "/")), n = 1)) |
59 s_name <- tools::file_path_sans_ext(basename(files)) | 61 s_name <- tools::file_path_sans_ext(basename(files)) |
60 pd <- data.frame(sample_name=s_name, sample_group=s_groups, stringsAsFactors=FALSE) | 62 pd <- data.frame(sample_name = s_name, sample_group = s_groups, stringsAsFactors = FALSE) |
61 print(pd) | 63 print(pd) |
62 | 64 |
63 cat("\t\t\tLoad Raw Data\n") | 65 cat("\t\t\tLoad Raw Data\n") |
64 raw_data <- readMSData(files=files, pdata = new("NAnnotatedDataFrame", pd), mode="onDisk") | 66 raw_data <- readMSData(files = files, pdata = new("NAnnotatedDataFrame", pd), mode = "onDisk") |
65 | 67 |
66 # Transform the files absolute pathways into relative pathways | 68 # Transform the files absolute pathways into relative pathways |
67 raw_data@processingData@files <- sub(paste(getwd(), "/", sep="") , "", raw_data@processingData@files) | 69 raw_data@processingData@files <- sub(paste(getwd(), "/", sep = ""), "", raw_data@processingData@files) |
68 | 70 |
69 # Create a sampleMetada file | 71 # Create a sampleMetada file |
70 sampleNamesList <- getSampleMetadata(xdata=raw_data, sampleMetadataOutput="sampleMetadata.tsv") | 72 sampleNamesList <- getSampleMetadata(xdata = raw_data, sampleMetadataOutput = "sampleMetadata.tsv") |
71 | |
72 #cat("\t\t\tCompute and Store TIC and BPI\n") | |
73 #chromTIC <- chromatogram(raw_data, aggregationFun = "sum") | |
74 #chromBPI <- chromatogram(raw_data, aggregationFun = "max") | |
75 | 73 |
76 cat("\n\n") | 74 cat("\n\n") |
77 | 75 |
78 # ----- EXPORT ----- | 76 # ----- EXPORT ----- |
79 | 77 |
83 print(raw_data@phenoData@data) | 81 print(raw_data@phenoData@data) |
84 cat("\n\n") | 82 cat("\n\n") |
85 | 83 |
86 #saving R data in .Rdata file to save the variables used in the present tool | 84 #saving R data in .Rdata file to save the variables used in the present tool |
87 objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") | 85 objects2save <- c("raw_data", "zipfile", "singlefile", "md5sumList", "sampleNamesList") #, "chromTIC", "chromBPI") |
88 save(list=objects2save[objects2save %in% ls()], file="readmsdata.RData") | 86 save(list = objects2save[objects2save %in% ls()], file = "readmsdata.RData") |
89 | 87 |
90 | 88 |
91 cat("\tDONE\n") | 89 cat("\tDONE\n") |