Mercurial > repos > tomnl > mspurity_averagefragspectra

annotate dimsPredictPuritySingle.R @ 15:42bfb67c3b62 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:33:15 +0000
parents b82a7c818839
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1 library(msPurity)
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2 library(optparse)
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3 print(sessionInfo())
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5 option_list <- list(
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6 make_option(c("--mzML_file"), type="character"),
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7 make_option(c("--mzML_files"), type="character"),
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8 make_option(c("--mzML_filename"), type="character", default=''),
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9 make_option(c("--mzML_galaxy_names"), type="character", default=''),
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10 make_option(c("--peaks_file"), type="character"),
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11 make_option(c("-o", "--out_dir"), type="character"),
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12 make_option("--minoffset", default=0.5),
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13 make_option("--maxoffset", default=0.5),
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14 make_option("--ilim", default=0.05),
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15 make_option("--ppm", default=4),
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16 make_option("--dimspy", action="store_true"),
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17 make_option("--sim", action="store_true"),
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18 make_option("--remove_nas", action="store_true"),
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19 make_option("--iwNorm", default="none", type="character"),
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20 make_option("--file_num_dimspy", default=1),
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21 make_option("--exclude_isotopes", action="store_true"),
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22 make_option("--isotope_matrix", type="character")
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23 )
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25 # store options
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26 opt<- parse_args(OptionParser(option_list=option_list))
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28 print(sessionInfo())
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29 print(opt)
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31 print(opt$mzML_files)
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32 print(opt$mzML_galaxy_names)
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34 str_to_vec <- function(x){
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35 print(x)
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36 x <- trimws(strsplit(x, ',')[[1]])
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37 return(x[x != ""])
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38 }
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39
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40 find_mzml_file <- function(mzML_files, galaxy_names, mzML_filename){
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41 mzML_filename <- trimws(mzML_filename)
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42 mzML_files <- str_to_vec(mzML_files)
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43 galaxy_names <- str_to_vec(galaxy_names)
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44 if (mzML_filename %in% galaxy_names){
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45 return(mzML_files[galaxy_names==mzML_filename])
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46 }else{
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47 stop(paste("mzML file not found - ", mzML_filename))
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48 }
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49 }
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52 if (is.null(opt$dimspy)){
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53 df <- read.table(opt$peaks_file, header = TRUE, sep='\t')
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54 if (file.exists(opt$mzML_file)){
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55 mzML_file <- opt$mzML_file
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56 }else if (!is.null(opt$mzML_files)){
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57 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names,
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58 opt$mzML_filename)
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59 }else{
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60 mzML_file <- file.path(opt$mzML_file, filename)
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61 }
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62 }else{
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63 indf <- read.table(opt$peaks_file,
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64 header = TRUE, sep='\t', stringsAsFactors = FALSE)
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65
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66 filename <- colnames(indf)[8:ncol(indf)][opt$file_num_dimspy]
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67 print(filename)
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68 # check if the data file is mzML or RAW (can only use mzML currently) so
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69 # we expect an mzML file of the same name in the same folder
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70 indf$i <- indf[,colnames(indf)==filename]
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71 indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename])
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73 filename = sub("raw", "mzML", filename, ignore.case = TRUE)
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74 print(filename)
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77 if (file.exists(opt$mzML_file)){
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78 mzML_file <- opt$mzML_file
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79 }else if (!is.null(opt$mzML_files)){
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80 mzML_file <- find_mzml_file(opt$mzML_files, opt$mzML_galaxy_names, filename)
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81 }else{
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82 mzML_file <- file.path(opt$mzML_file, filename)
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83 }
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84
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85 # Update the dimspy output with the correct information
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86 df <- indf[4:nrow(indf),]
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87 if ('blank_flag' %in% colnames(df)){
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88 df <- df[df$blank_flag==1,]
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89 }
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90 colnames(df)[colnames(df)=='m.z'] <- 'mz'
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92 if ('nan' %in% df$mz){
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93 df[df$mz=='nan',]$mz <- NA
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94 }
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95 df$mz <- as.numeric(df$mz)
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96 }
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97
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98 if (!is.null(opt$remove_nas)){
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99 df <- df[!is.na(df$mz),]
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100 }
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101
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102 if (is.null(opt$isotope_matrix)){
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103 im <- NULL
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104 }else{
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105 im <- read.table(opt$isotope_matrix,
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106 header = TRUE, sep='\t', stringsAsFactors = FALSE)
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107 }
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108
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109 if (is.null(opt$exclude_isotopes)){
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110 isotopes <- FALSE
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111 }else{
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112 isotopes <- TRUE
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113 }
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114
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115 if (is.null(opt$sim)){
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116 sim=FALSE
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117 }else{
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118 sim=TRUE
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119 }
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120
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121 minOffset = as.numeric(opt$minoffset)
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122 maxOffset = as.numeric(opt$maxoffset)
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123
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124 if (opt$iwNorm=='none'){
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125 iwNorm = FALSE
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126 iwNormFun = NULL
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127 }else if (opt$iwNorm=='gauss'){
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128 iwNorm = TRUE
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129 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
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130 }else if (opt$iwNorm=='rcosine'){
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131 iwNorm = TRUE
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132 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
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133 }else if (opt$iwNorm=='QE5'){
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134 iwNorm = TRUE
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135 iwNormFun = msPurity::iwNormQE.5()
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136 }
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137
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138 print('FIRST ROWS OF PEAK FILE')
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139 print(head(df))
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140 print(mzML_file)
0
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141 predicted <- msPurity::dimsPredictPuritySingle(df$mz,
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142 filepth=mzML_file,
0
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143 minOffset=minOffset,
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144 maxOffset=maxOffset,
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145 ppm=opt$ppm,
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146 mzML=TRUE,
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147 sim = sim,
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148 ilim = opt$ilim,
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149 isotopes = isotopes,
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150 im = im,
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151 iwNorm = iwNorm,
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152 iwNormFun = iwNormFun
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153 )
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154 predicted <- cbind(df, predicted)
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155
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156 print(head(predicted))
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157 print(file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'))
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158
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159 write.table(predicted,
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160 file.path(opt$out_dir, 'dimsPredictPuritySingle_output.tsv'),
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161 row.names=FALSE, sep='\t')
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162
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163