Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter_wrapper.R @ 12:38f509903a0b draft

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
author eschen42
date Tue, 01 Oct 2019 16:57:58 -0400
parents d5cf23369d12
children c18040b6e8b9
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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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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") < "0.98.12")
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27 stop("Please use 'w4mclassfilter' versions of 0.98.12 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 my_print <- function(x, ...) { cat(c(x, ...))}
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65
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66 my_print("\nStart of the '", modNamC, "' Galaxy module call: ",
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67 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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68
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69 ## arguments
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70 ##----------
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71
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72 # files
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73
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74 dataMatrix_in <- as.character(argVc["dataMatrix_in"])
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75 dataMatrix_out <- as.character(argVc["dataMatrix_out"])
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76
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77 sampleMetadata_in <- as.character(argVc["sampleMetadata_in"])
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78 sampleMetadata_out <- as.character(argVc["sampleMetadata_out"])
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79
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80 variableMetadata_in <- as.character(argVc["variableMetadata_in"])
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81 variableMetadata_out <- as.character(argVc["variableMetadata_out"])
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82
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83 # other parameters
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84
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85 transformation <- as.character(argVc["transformation"])
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86 my_imputation_label <- as.character(argVc["imputation"])
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87 my_imputation_function <- if (my_imputation_label == "zero") {
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88 w4m_filter_zero_imputation
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89 } else if (my_imputation_label == "center") {
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90 w4m_filter_median_imputation
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91 } else if (my_imputation_label == "none") {
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92 w4m_filter_no_imputation
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93 } else {
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94 stop(sprintf("Unknown value %s supplied for 'imputation' parameter. Expected one of {zero,center,none}."))
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95 }
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96 wildcards <- as.logical(argVc["wildcards"])
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97 sampleclassNames <- as.character(argVc["sampleclassNames"])
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98 sampleclassNames <- strsplit(x = sampleclassNames, split = ",", fixed = TRUE)[[1]]
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99 if (wildcards) {
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100 sampleclassNames <- gsub("[.]", "[.]", sampleclassNames)
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101 sampleclassNames <- utils::glob2rx(sampleclassNames, trim.tail = FALSE)
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102 }
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103 inclusive <- as.logical(argVc["inclusive"])
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104 classnameColumn <- as.character(argVc["classnameColumn"])
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105 samplenameColumn <- as.character(argVc["samplenameColumn"])
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106
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107 variable_range_filter <- as.character(argVc["variable_range_filter"])
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108 variable_range_filter <- strsplit(x = variable_range_filter, split = ",", fixed = TRUE)[[1]]
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109
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110 ## -----------------------------
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111 ## Transformation and imputation
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112 ## -----------------------------
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113 my_transformation_and_imputation <- if (transformation == "log10") {
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114 function(m) {
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115 if (!is.matrix(m))
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116 stop("Cannot transform and impute data - the supplied data is not in matrix form")
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117 if (nrow(m) == 0)
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118 stop("Cannot transform and impute data - data matrix has no rows")
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119 if (ncol(m) == 0)
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120 stop("Cannot transform and impute data - data matrix has no columns")
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121 suppressWarnings({
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122 # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
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123 m <- log10(m)
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124 m[is.na(m)] <- NA
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125 })
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126 return ( my_imputation_function(m) )
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127 }
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128 } else if (transformation == "log2") {
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129 function(m) {
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130 if (!is.matrix(m))
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131 stop("Cannot transform and impute data - the supplied data is not in matrix form")
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132 if (nrow(m) == 0)
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133 stop("Cannot transform and impute data - data matrix has no rows")
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134 if (ncol(m) == 0)
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135 stop("Cannot transform and impute data - data matrix has no columns")
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136 suppressWarnings({
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137 # suppress warnings here since non-positive values will produce NaN's that will be fixed in the next step
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138 m <- log2(m)
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139 m[is.na(m)] <- NA
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140 })
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141 return ( my_imputation_function(m) )
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142 }
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143 } else {
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144 # use the method from the w4mclassfilter class
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145 my_imputation_function
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146 }
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147
0
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148 ##------------------------------
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149 ## Computation
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150 ##------------------------------
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151
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152 result <- w4m_filter_by_sample_class(
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153 dataMatrix_in = dataMatrix_in
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154 , sampleMetadata_in = sampleMetadata_in
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155 , variableMetadata_in = variableMetadata_in
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156 , dataMatrix_out = dataMatrix_out
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157 , sampleMetadata_out = sampleMetadata_out
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158 , variableMetadata_out = variableMetadata_out
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159 , classes = sampleclassNames
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160 , include = inclusive
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161 , class_column = classnameColumn
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162 , samplename_column = samplenameColumn
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163 , variable_range_filter = variable_range_filter
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164 , failure_action = my_print
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165 , data_imputation = my_transformation_and_imputation
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166 )
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167
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168 my_print("\nResult of '", modNamC, "' Galaxy module call to 'w4mclassfilter::w4m_filter_by_sample_class' R function: ",
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169 as.character(result), "\n", sep = "")
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170
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171 ##--------
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172 ## Closing
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173 ##--------
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174
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175 my_print("\nEnd of '", modNamC, "' Galaxy module call: ",
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176 as.character(Sys.time()), "\n", sep = "")
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177
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178 #sink()
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179
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180 if (!file.exists(dataMatrix_out)) {
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181 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, dataMatrix_out))
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182 }# else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, dataMatrix_out)) }
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183
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184 if (!file.exists(variableMetadata_out)) {
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185 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, variableMetadata_out))
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186 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, variableMetadata_out)) }
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187
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188 if (!file.exists(sampleMetadata_out)) {
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189 print(sprintf("ERROR %s::w4m_filter_by_sample_class - file '%s' was not created", modNamC, sampleMetadata_out))
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190 } # else { print(sprintf("INFO %s::w4m_filter_by_sample_class - file '%s' was exists", modNamC, sampleMetadata_out)) }
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191
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192 if( !result ) {
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193 stop(sprintf("ERROR %s::w4m_filter_by_sample_class - method failed", modNamC))
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194 }
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195
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196 rm(list = ls())