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comparison BC/batch_correction_3Lwrapper.R @ 4:23314e1192d4 draft default tip

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author melpetera
date Thu, 14 Jan 2021 09:56:58 +0000
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3:73892ef177e3 4:23314e1192d4
1 #!/usr/bin/env Rscript
2
3 ################################################################################################
4 # batch_correction_wrapper #
5 # #
6 # Authors: Marion LANDI / Jean-Francois MARTIN / Melanie Petera #
7 # User: Galaxy #
8 # Original data: -- #
9 # Starting date: 22-07-2014 #
10 # Version 1: 22-07-2014 #
11 # Version 2: 08-12-2014 #
12 # Version 2.1: 09-01-2015 modification in Error message of sample matching #
13 # Version 2.2: 16-03-2015 inclusion of miniTools' functions for special characters #
14 # Version 2.90: 18-08-2015 new parameter valnull #
15 # Version 2.91: 25-08-2016 error message improvment #
16 # Version 3: 02-10-2020 #
17 # - split of tool-linked code and script-linked one #
18 # - addition of args print and sessionInfo() #
19 # - adjustment of sample tags' parameters to 3L methods #
20 # - addition of the min.norm argument in meth3L() call #
21 # #
22 # Input files: dataMatrix.txt, sampleMetadata.txt, variableMetadata.txt (BC only) #
23 # Output files: graph.pdf, corrected table (BC only), diagnostic table (DBC only), #
24 # variableMetadata (BC only) #
25 # #
26 ################################################################################################
27
28
29 library(batch) #necessary for parseCommandArgs function
30
31 ##------------------------------
32 ## test help option
33 ##------------------------------
34
35 # Prog. constants
36 argv.help <- commandArgs(trailingOnly = FALSE)
37 script.path <- sub("--file=", "", argv.help[grep("--file=", argv.help)])
38 prog.name <- basename(script.path)
39
40 # Test Help
41 if (length(grep('-h', argv.help)) > 0) {
42 cat("Usage: Rscript ",
43 prog.name,
44 "{args} \n",
45 "parameters: \n",
46 "\tanalyse {val}: must be set to \"batch_correction\"",
47 "\tdataMatrix {file}: set the input data matrix file (mandatory) \n",
48 "\tsampleMetadata {file}: set the input sample metadata file (mandatory) \n",
49 "\tvariableMetadata {file}: set the input variable metadata file (mandatory) \n",
50 "\tmethod {opt}: set the method; can set to \"linear\", \"lowess\" or \"loess\" (mandatory) \n",
51 "\tspan {condition}: set the span condition; set to \"none\" if method is set to \"linear\" (mandatory) \n",
52 "\tref_factor {value}: set the ref_factor value; (if span value is set to NULL, optional) \n",
53 "\tdetail {value}: set the detail value; (if span value is set to NULL, optional) \n",
54 "\tdataMatrix_out {file}: set the output data matrix file (mandatory) \n",
55 "\tvariableMetadata_out {file}: set the output variable metadata file (mandatory) \n",
56 "\tgraph_output {file}: set the output graph file (mandatory) \n",
57 "\trdata_output {file}: set the output Rdata file (mandatory) \n",
58 "\tbatch_col_name {val}: the column name for batch. Default value is \"batch\".\n",
59 "\tinjection_order_col_name {val}: the column name for the injection order. Default value is \"injectionOrder\".\n",
60 "\tsample_type_col_name {val}: the column name for the sample types. Default value is \"sampleType\".\n",
61 "\tsample_type_tags {val}: the tags used inside the sample type column, defined as key/value pairs separated by commas (example: blank=blank,pool=pool,sample=sample).\n",
62 "\n")
63 quit(status = 0)
64 }
65
66 ##------------------------------
67 ## init. params
68 ##------------------------------
69
70 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
71
72
73 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
74 '\n\n--------------------------------------------------------------------',
75 '\nParameters used:\n\n')
76 print(args)
77 cat('--------------------------------------------------------------------\n\n')
78
79
80 # Set default col names
81 if ( ! 'batch_col_name' %in% names(args))
82 args[['batch_col_name']] <- 'batch'
83 if ( ! 'injection_order_col_name' %in% names(args))
84 args[['injection_order_col_name']] <- 'injectionOrder'
85 if ( ! 'sample_type_col_name' %in% names(args))
86 args[['sample_type_col_name']] <- 'sampleType'
87 if ( ! 'sample_type_tags' %in% names(args))
88 args[['sample_type_tags']] <- 'blank=blank,pool=pool,sample=sample'
89
90 # Parse sample type tags
91 sample.type.tags <- list()
92 for (kv in strsplit(strsplit(args$sample_type_tags, ',')[[1]], '='))
93 sample.type.tags[[kv[[1]]]] <- kv[-1]
94 if ( ! all(c('pool', 'blank', 'sample') %in% names(sample.type.tags)))
95 stop("All tags pool, blank and sample must be defined in option sampleTypeTags.")
96 args$sample_type_tags <- sample.type.tags
97
98 ##------------------------------
99 ## init. functions
100 ##------------------------------
101
102 source_local <- function(...){
103 argv <- commandArgs(trailingOnly = FALSE)
104 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
105 for(i in 1:length(list(...))){source(paste(base_dir, list(...)[[i]], sep="/"))}
106 }
107 #Import the different functions
108 source_local("batch_correction_3Lfct.R","batch_correction_3Llauncher.R","easyrlibrary-lib/RcheckLibrary.R","easyrlibrary-lib/miniTools.R")
109
110 # Specificities of BC and DBC
111 if(args$analyse == "batch_correction") {
112 args$out_graph_pdf <- NULL
113 args$out_preNormSummary <- NULL
114 }else{
115 args$variableMetadata <- NULL
116 args$rdata_output <- NULL
117 args$dataMatrix_out <- NULL
118 args$variableMetadata_out <- NULL
119 args$graph_output <- NULL
120 args$method <- NULL
121 args$detail <- NULL
122 args$valnull <- NULL
123 }
124
125 # Launch tool
126 meth3L(idsample=args$sampleMetadata, iddata=args$dataMatrix, sample_type_col_name=args$sample_type_col_name, injection_order_col_name=args$injection_order_col_name,
127 batch_col_name=args$batch_col_name, sample_type_tags=args$sample_type_tags, factbio=args$ref_factor, analyse=args$analyse, metaion=args$variableMetadata,
128 detail=args$detail, method=args$method, outlog=args$graph_output, span=args$span, valnull=args$valnull, rdata_output=args$rdata_output,
129 dataMatrix_out=args$dataMatrix_out, variableMetadata_out=args$variableMetadata_out, out_graph_pdf=args$out_graph_pdf, out_preNormSummary=args$out_preNormSummary,
130 min.norm=1)
131
132
133 cat('\n\n--------------------------------------------------------------------',
134 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
135 sessionInfo()
136 cat('--------------------------------------------------------------------\n',
137 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
138
139 rm(args)