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1 #!/usr/bin/env Rscript
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2
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3 library(batch) ## parseCommandArgs
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4
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5 ########
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6 # MAIN #
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7 ########
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8
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9 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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10
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11 ##------------------------------
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12 ## Initializing
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13 ##------------------------------
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14
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15 ## options
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16 ##--------
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17
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18 strAsFacL <- options()$stringsAsFactors
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19 options(stringsAsFactors = FALSE)
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20
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21 ## libraries
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22 ##----------
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23
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24 suppressMessages(library(w4mclassfilter))
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25
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26 if(packageVersion("w4mclassfilter") < "0.98.0")
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27 stop("Please use 'w4mclassfilter' versions of 0.98.0 and above")
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28
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29 ## constants
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30 ##----------
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31
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32 modNamC <- "w4mclassfilter" ## module name
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33
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34 topEnvC <- environment()
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35 flgC <- "\n"
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36
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37 ## functions
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38 ##----------
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39
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40 flgF <- function(tesC,
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41 envC = topEnvC,
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42 txtC = NA) { ## management of warning and error messages
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43
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44 tesL <- eval(parse(text = tesC), envir = envC)
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45
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46 if(!tesL) {
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47
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48 #sink(NULL)
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49 stpTxtC <- ifelse(is.na(txtC),
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50 paste0(tesC, " is FALSE"),
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51 txtC)
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52
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53 stop(stpTxtC,
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54 call. = FALSE)
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55
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56 }
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57
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58 } ## flgF
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59
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60
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61 ## log file
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62 ##---------
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63
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64 information <- as.character(argVc["information"])
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65
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66 #sink(information)
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67
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68 my_print <- function(x, ...) { cat(c(x, ...))}
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69
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70 my_print("\nStart of the '", modNamC, "' Galaxy module call: ",
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71 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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72
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73 ## arguments
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74 ##----------
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75
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76 # files
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77
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78 dataMatrix_in <- as.character(argVc["dataMatrix_in"])
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79 dataMatrix_out <- as.character(argVc["dataMatrix_out"])
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80
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81 sampleMetadata_in <- as.character(argVc["sampleMetadata_in"])
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82 sampleMetadata_out <- as.character(argVc["sampleMetadata_out"])
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83
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84 variableMetadata_in <- as.character(argVc["variableMetadata_in"])
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85 variableMetadata_out <- as.character(argVc["variableMetadata_out"])
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86
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87 # other parameters
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88
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89 sampleclassNames <- as.character(argVc["sampleclassNames"])
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90 # if (sampleclassNames == "NONE_SPECIFIED") {
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91 # sampleclassNames <- as.character(c())
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92 #
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93 # } else {
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94 # sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
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95 # }
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96 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
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97 inclusive <- as.logical(argVc["inclusive"])
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98 # print(sprintf("inclusive = '%s'", as.character(inclusive)))
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99 classnameColumn <- as.character(argVc["classnameColumn"])
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100 samplenameColumn <- as.character(argVc["samplenameColumn"])
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101
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102 ##------------------------------
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103 ## Computation
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104 ##------------------------------
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105
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106 result <- w4m_filter_by_sample_class(
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107 dataMatrix_in = dataMatrix_in
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108 , sampleMetadata_in = sampleMetadata_in
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109 , variableMetadata_in = variableMetadata_in
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110 , dataMatrix_out = dataMatrix_out
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111 , sampleMetadata_out = sampleMetadata_out
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112 , variableMetadata_out = variableMetadata_out
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113 , classes = sampleclassNames
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114 , include = inclusive
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115 , class_column = classnameColumn
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116 , samplename_column = samplenameColumn
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117 , failure_action = my_print
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118 )
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119
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120 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",
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121 as.character(result), "\n", sep = "")
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122
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123 ##--------
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124 ## Closing
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125 ##--------
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126
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127 my_print("\nEnd of '", modNamC, "' Galaxy module call: ",
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128 as.character(Sys.time()), "\n", sep = "")
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129
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130 #sink()
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131
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132 if (!file.exists(dataMatrix_out)) {
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133 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out))
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134 }# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) }
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135
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136 if (!file.exists(variableMetadata_out)) {
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137 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out))
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138 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) }
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139
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140 if (!file.exists(sampleMetadata_out)) {
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141 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out))
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142 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) }
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143
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144 if( !result ) {
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145 stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
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146 }
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147
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148 rm(list = ls())
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