annotate MS2snoop.R @ 1:df2672c37732 draft

planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
author workflow4metabolomics
date Tue, 24 May 2022 18:14:49 +0000
parents 91a3242fd67f
children c68c94865667
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1 #'
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2 #' read and process mspurity W4M files
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3 #' create a summary of fragment for each precursor and a graphics of peseudo
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4 #' spectra + correlation on which checking of fragment is based on
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5 #' V3 try to identify and process multiple files for 1 precursor which may
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6 #' occur if different collision energy are used
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7 #' V4 elimination of correlation = NA. Correlation is done with precursor, if
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8 #' precursor is not present correlation with most intense peak
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9 #' author: Jean-Francois Martin
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10 #' V5 is versionned, lintR-compliant, packaged, unit-tested, documented and
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11 #' tested against data from other labs.
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12 #' new maintainer: Lain Pavot - lain.pavot@inrae.fr
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13 #'
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14 #' @import optparse
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15 #'
1
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18 assign("MS2SNOOP_VERSION", "1.0.1")
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19 lockBinding("MS2SNOOP_VERSION", globalenv())
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20
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21 assign("MISSING_PARAMETER_ERROR", 1)
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22 lockBinding("MISSING_PARAMETER_ERROR", globalenv())
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23
1
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24 assign("BAD_PARAMETER_VALUE_ERROR", 2)
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25 lockBinding("BAD_PARAMETER_VALUE_ERROR", globalenv())
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27 assign("MISSING_INPUT_FILE_ERROR", 3)
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28 lockBinding("MISSING_INPUT_FILE_ERROR", globalenv())
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30 assign("NO_ANY_RESULT_ERROR", 255)
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31 lockBinding("NO_ANY_RESULT_ERROR", globalenv())
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33 assign("DEFAULT_PRECURSOR_PATH", "peaklist_precursors.tsv")
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34 assign("DEFAULT_FRAGMENTS_PATH", "peaklist_fragments.tsv")
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35 assign("DEFAULT_COMPOUNDS_PATH", "compounds_pos.txt")
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36 assign("DEFAULT_OUTPUT_PATH", "compound_fragments_result.txt")
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37 assign("DEFAULT_TOLMZ", 0.01)
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38 assign("DEFAULT_TOLRT", 20)
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39 assign("DEFAULT_MZDECIMAL", 0)
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40 assign("DEFAULT_R_THRESHOLD", 0.85)
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41 assign("DEFAULT_MINNUMBERSCAN", 8)
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42 assign("DEFAULT_SEUIL_RA", 0.5)
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43 lockBinding("DEFAULT_PRECURSOR_PATH", globalenv())
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44 lockBinding("DEFAULT_FRAGMENTS_PATH", globalenv())
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45 lockBinding("DEFAULT_COMPOUNDS_PATH", globalenv())
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46 lockBinding("DEFAULT_OUTPUT_PATH", globalenv())
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47 lockBinding("DEFAULT_TOLMZ", globalenv())
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48 lockBinding("DEFAULT_TOLRT", globalenv())
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49 lockBinding("DEFAULT_MZDECIMAL", globalenv())
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50 lockBinding("DEFAULT_R_THRESHOLD", globalenv())
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51 lockBinding("DEFAULT_MINNUMBERSCAN", globalenv())
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52 lockBinding("DEFAULT_SEUIL_RA", globalenv())
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53
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54 assign("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", 0.85)
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55 assign("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", 0.1)
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56 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", 0.01)
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57 assign("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", 60)
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58 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD", globalenv())
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59 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA", globalenv())
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60 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLMZ", globalenv())
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61 lockBinding("DEFAULT_EXTRACT_FRAGMENTS_TOLRT", globalenv())
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62
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63
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64 ########################################################################
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65
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66 #' @title plot_pseudo_spectra
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67 #' @param x
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68 #' @param r_threshold
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69 #' @param fid
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70 #' @param sum_int
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71 #' @param vmz
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72 #' @param cor_abs_int
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73 #' @param refcol
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74 #' @param c_name
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75 #' @description plot_pseudo_spectra
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76 #' function to compute sum of intensities among scans for all
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77 #' m/z kept (cor > r_threshold & minimum number of scans)
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78 #' and plot pseudo spectra
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79 #' x dataframe scan X fragments with scans number in the 1st column and
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80 #' ions in next with intensities
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81 #' fid file id when several a precursor has been detected in several files
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82 plot_pseudo_spectra <- function(
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83 x,
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84 r_threshold,
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85 fid,
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86 sum_int,
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87 vmz,
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88 cor_abs_int,
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89 refcol,
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90 c_name
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91 ) {
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92 ## du fait de la difference de nombre de colonne entre la dataframe qui
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93 ## inclue les scans en 1ere col, mzRef se decale de 1
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94 refcol <- refcol - 1
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95 ## compute relative intensities max=100%
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96 rel_int <- sum_int[-1]
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97 rel_int <- rel_int / max(rel_int)
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98
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99 ## define max value on vertical axis (need to increase in order to plot the
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100 ## label of fragments)
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101 ymax <- max(rel_int) + 0.2 * max(rel_int)
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102
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103 par(mfrow = c(2, 1))
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104 plot(vmz, rel_int, type = "h", ylim = c(0, ymax), main = c_name)
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105 ## low correl coef. will be display in grey
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106 cor_low <- which(round(cor_abs_int, 2) < r_threshold)
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107
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108 lbmzcor <- sprintf("%s(r=%s)", vmz, round(cor_abs_int, 2))
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109
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110 if (length(cor_low) > 0) {
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111 text(
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112 vmz[cor_low],
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113 rel_int[cor_low],
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114 lbmzcor[cor_low],
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115 cex = 0.5,
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116 col = "grey",
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117 srt = 90,
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118 adj = 0
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119 )
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120 if (length(vmz) - length(cor_low) > 1) {
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121 text(
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122 vmz[-c(refcol, cor_low)],
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123 rel_int[-c(refcol, cor_low)],
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124 lbmzcor[-c(refcol, cor_low)],
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125 cex = 0.6,
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126 col = 1,
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127 srt = 90,
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128 adj = 0
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129 )
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130 }
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131 } else {
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132 if (length(vmz) > 1) {
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133 text(
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134 vmz[-c(refcol)],
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135 rel_int[-c(refcol)],
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136 lbmzcor[-c(refcol)],
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137 cex = 0.6,
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138 col = 1,
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139 srt = 90,
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140 adj = 0
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141 )
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142 }
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143 }
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144
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145 text(
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146 vmz[refcol],
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147 rel_int[refcol],
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148 lbmzcor[refcol],
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149 cex = 0.8,
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150 col = 2,
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151 srt = 90,
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152 adj = 0
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153 )
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154
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155 ## prepare result file
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156 corValid <- (round(cor_abs_int, 2) >= r_threshold) ##nolint object_name_linter
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157 cp_res <- data.frame(
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158 rep(c_name, length(vmz)),
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159 rep(fid, length(vmz)),
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160 vmz,
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161 cor_abs_int,
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162 sum_int[-1],
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163 rel_int,
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164 corValid
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165 )
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166
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167 colnames(cp_res) <- c(
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168 "compoundName",
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169 "fileid",
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170 "fragments_mz",
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171 "CorWithPrecursor",
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172 "AbsoluteIntensity",
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173 "relativeIntensity",
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174 "corValid"
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175 )
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176 return(cp_res)
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177
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178 }
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179
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180 #'
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181 #' @title extract_fragments
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182 #'
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183 #' @param precursors the precursor list from mspurity
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184 #' @param fragments the fragments list from ms purity
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185 #' @param mzref
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186 #' @param rtref
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187 #' @param c_name
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188 #' @param r_threshold default = DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD
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189 #' @param seuil_ra default = DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA
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190 #' @param tolmz default = DEFAULT_EXTRACT_FRAGMENTS_TOLMZ
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191 #' @param tolrt default = DEFAULT_EXTRACT_FRAGMENTS_TOLRT
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192 #' @returns
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193 #'
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194 #' @description
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195 #' function for extraction of fragments corresponding to precursors
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196 #' detected by MSPurity
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197 extract_fragments <- function( ## nolint cyclocomp_linter
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198 precursors,
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199 fragments,
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200 mzref,
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201 rtref,
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202 c_name,
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203 min_number_scan,
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204 mzdecimal,
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205 r_threshold=DEFAULT_EXTRACT_FRAGMENTS_R_THRESHOLD,
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206 seuil_ra=DEFAULT_EXTRACT_FRAGMENTS_SEUIL_RA,
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207 tolmz=DEFAULT_EXTRACT_FRAGMENTS_TOLMZ,
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208 tolrt=DEFAULT_EXTRACT_FRAGMENTS_TOLRT
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209 ) {
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210 ## filter precursor in the precursors file based on mz and rt in the
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211 ## compound list
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212 cat("processing ", c_name, "\n")
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213 selected_precursors <- which(
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214 (abs(precursors$precurMtchMZ - mzref) <= tolmz)
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215 & (abs(precursors$precurMtchRT - rtref) <= tolrt)
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216 )
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217
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218 ## check if there is the precursor in the file
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219 if (length(selected_precursors) > 0) {
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220
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221 sprecini <- precursors[selected_precursors, ]
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222
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223 ## check if fragments corresponding to precursor are found in several
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224 ## files (collision energy)
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225 ## this lead to a processing for each fileid
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226 mf <- levels(as.factor(sprecini$fileid))
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227 if (length(mf) > 1 && global_verbose) {
0
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228 cat(" several files detected for this compounds :\n")
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229 }
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230
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231 for (f in seq_along(mf)) {
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232
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233 sprec <- sprecini[sprecini$fileid == mf[f], ]
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234
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235 ## selection of fragment in the fragments file with the grpid common in
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236 ## both fragments and precursors
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237 selfrgt <- levels(as.factor(sprec$grpid))
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238 sfrgt <- fragments[
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239 fragments$grpid %in% selfrgt
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240 & fragments$fileid == mf[f],
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241 ]
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242
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243 ## filter fragments on relative intensity seuil_ra = user defined
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244 ## parameter (MSpurity flags could be used here)
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245 sfrgtfil <- sfrgt[sfrgt$ra > seuil_ra, ]
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246
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247 mznominal <- round(x = sfrgtfil$mz, mzdecimal)
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248 sfrgtfil <- data.frame(sfrgtfil, mznominal)
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249
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250 ## creation of cross table row=scan col=mz X=ra
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251 vmz <- levels(as.factor(sfrgtfil$mznominal))
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252
1
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253 if (global_verbose) {
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254 cat(" fragments :", vmz)
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255 }
0
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256
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257 ## mz of precursor in data precursor to check correlation with
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258 mz_prec <- paste0("mz", round(mean(sprec$mz), mzdecimal))
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259
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260 for (m in seq_along(vmz)) {
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261
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262 ## absolute intensity
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263 cln <- c(
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264 which(colnames(sfrgtfil) == "acquisitionNum"),
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265 which(colnames(sfrgtfil) == "i")
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266 )
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267 int_mz <- sfrgtfil[sfrgtfil$mznominal == vmz[m], cln]
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268 colnames(int_mz)[2] <- paste0("mz", vmz[m])
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269
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270 ## average intensities of mass in duplicate scans
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271 comp_scans <- aggregate(x = int_mz, by = list(int_mz[[1]]), FUN = mean)
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272 int_mz <- comp_scans[, -1]
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273
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274 if (m == 1) {
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275 ds_abs_int <- int_mz
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276 } else {
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277 ds_abs_int <- merge(
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278 x = ds_abs_int,
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279 y = int_mz,
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280 by.x = 1,
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281 by.y = 1,
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282 all.x = TRUE,
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283 all.y = TRUE
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284 )
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285 }
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286 }
1
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287 if (global_debug) {
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288 print(ds_abs_int)
0
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289 write.table(
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290 x = ds_abs_int,
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291 file = paste0(c_name, "ds_abs_int.txt"),
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292 row.names = FALSE,
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293 sep = "\t"
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294 )
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295 }
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296
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297 ## elimination of mz with less than min_number_scan scans (user defined
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298 ## parameter)
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299 xmz <- rep(NA, ncol(ds_abs_int) - 1)
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300 sum_int <- rep(NA, ncol(ds_abs_int))
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301 nbxmz <- 0
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302 nb_scan_check <- min(nrow(ds_abs_int), min_number_scan)
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303
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304 for (j in 2:ncol(ds_abs_int)) {
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305 sum_int[j] <- sum(ds_abs_int[j], na.rm = TRUE)
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306 if (sum(!is.na(ds_abs_int[[j]])) < nb_scan_check) {
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307 nbxmz <- nbxmz + 1
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308 xmz[nbxmz] <- j
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309 }
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310 }
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311
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312 xmz <- xmz[-which(is.na(xmz))]
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313 if (length(xmz) > 0) {
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314 ds_abs_int <- ds_abs_int[, -c(xmz)]
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315 sum_int <- sum_int[-c(xmz)]
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316 ## liste des mz keeped decale de 1 avec ds_abs_int
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317 vmz <- as.numeric(vmz[-c(xmz - 1)])
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318 }
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319
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320 ## reference ion for correlation computing = precursor OR maximum
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321 ## intensity ion in precursor is not present
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322 refcol <- which(colnames(ds_abs_int) == mz_prec)
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323 if (length(refcol) == 0) {
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324 refcol <- which(sum_int == max(sum_int, na.rm = TRUE))
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325 }
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326 pdf(
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327 file = sprintf("%s_processing_file%s.pdf", c_name, mf[f]),
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328 width = 8,
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329 height = 11
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330 )
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331 par(mfrow = c(3, 2))
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332
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333 ## Pearson correlations between absolute intensities computing
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334 cor_abs_int <- rep(NA, length(vmz))
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335
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336 if (length(refcol) > 0) {
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337 for (i in 2:length(ds_abs_int)) {
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338 cor_abs_int[i - 1] <- cor(
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339 x = ds_abs_int[[refcol]],
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340 y = ds_abs_int[[i]],
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341 use = "pairwise.complete.obs",
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342 method = "pearson"
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343 )
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344 plot(
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345 ds_abs_int[[refcol]],
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346 ds_abs_int[[i]],
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347 xlab = colnames(ds_abs_int)[refcol],
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348 ylab = colnames(ds_abs_int)[i],
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349 main = sprintf(
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350 "%s corr coeff r=%s", c_name, round(cor_abs_int[i - 1], 2)
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351 )
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352 )
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353 }
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354 ## plot pseudo spectra
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355 res_comp_by_file <- plot_pseudo_spectra(
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356 x = ds_abs_int,
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357 r_threshold = r_threshold,
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358 fid = mf[f],
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359 sum_int = sum_int,
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360 vmz = vmz,
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361 cor_abs_int = cor_abs_int,
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362 refcol = refcol,
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363 c_name = c_name
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364 )
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365 if (f == 1) {
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366 res_comp <- res_comp_by_file
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367 }
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368 } else {
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369 res_comp_by_file <- NULL
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370 cat(" non detected in fragments file \n")
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371 }
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372 if (!is.null(res_comp_by_file)) {
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373 res_comp <- rbind(res_comp, res_comp_by_file)
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374 }
1
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375 if (global_verbose) {
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diff changeset
376 cat("\n")
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377 }
0
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378 dev.off()
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379 }
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380 } else {
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381 res_comp <- NULL
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382 cat(" non detected in precursor file \n")
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383 }
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384 return(res_comp)
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385 }
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386
1
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387 set_global <- function(var, value) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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388 assign(var, value, envir = globalenv())
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389 }
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390
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391 set_debug <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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392 set_global("global_debug", TRUE)
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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393 }
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394
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395 unset_debug <- function() {
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396 set_global("global_debug", FALSE)
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397 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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398
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399 set_verbose <- function() {
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400 set_global("global_verbose", TRUE)
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401 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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402
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403 unset_verbose <- function() {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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404 set_global("global_verbose", FALSE)
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405 }
0
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406
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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407 create_parser <- function() {
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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408 parser <- optparse::OptionParser()
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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409 parser <- optparse::add_option(
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410 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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411 c("-v", "--verbose"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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412 action = "store_true",
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413 default = FALSE,
1
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414 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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415 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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416 "Print extra output"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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417 )
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418 )
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419 parser <- optparse::add_option(
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420 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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421 c("-V", "--version"),
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422 action = "store_true",
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423 default = FALSE,
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424 help = "Prints version and exits"
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425 )
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426 parser <- optparse::add_option(
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427 parser,
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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428 c("-d", "--debug"),
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429 action = "store_true",
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430 default = FALSE,
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431 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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432 "[default %default]",
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433 "Print debug outputs"
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434 )
0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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435 )
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436 parser <- optparse::add_option(
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437 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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438 c("-o", "--output"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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439 type = "character",
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440 default = DEFAULT_OUTPUT_PATH,
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441 action = "store",
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442 help = "Path to the output file [default %default]"
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443 )
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444 parser <- optparse::add_option(
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445 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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446 c("-p", "--precursors"),
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447 type = "character",
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448 default = DEFAULT_PRECURSOR_PATH,
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449 action = "store",
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450 help = "Path to the precursors file [default %default]"
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451 )
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452 parser <- optparse::add_option(
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453 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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454 c("-f", "--fragments"),
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455 type = "character",
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456 default = DEFAULT_FRAGMENTS_PATH,
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457 action = "store",
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458 help = "Path to the fragments file [default %default]"
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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459 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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460 parser <- optparse::add_option(
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461 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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462 c("-c", "--compounds"),
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463 type = "character",
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464 default = DEFAULT_COMPOUNDS_PATH,
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465 action = "store",
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466 help = "Path to the compounds file [default %default]"
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467 )
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468 parser <- optparse::add_option(
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469 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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470 c("--tolmz"),
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471 type = "numeric",
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472 action = "store",
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473 default = DEFAULT_TOLMZ,
1
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474 metavar = "number",
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475 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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476 "[default %default]",
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477 "Tolerance for MZ (in Dalton) to match the standard in the compounds"
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478 )
0
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479 )
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480 parser <- optparse::add_option(
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481 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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482 c("--tolrt"),
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parents:
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483 type = "integer",
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484 action = "store",
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485 default = DEFAULT_TOLRT,
1
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486 metavar = "number",
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487 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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488 "[default %default]",
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489 "RT (in seconds) to match the standard in the compounds"
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diff changeset
490 )
0
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491 )
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492 parser <- optparse::add_option(
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493 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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494 c("--seuil_ra"),
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495 type = "numeric",
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496 action = "store",
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497 default = DEFAULT_SEUIL_RA,
1
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498 metavar = "number",
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499 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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500 "[default %default]",
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501 "relative intensity threshold"
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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502 ),
0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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503 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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504 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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505 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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506 c("--mzdecimal"),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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507 type = "integer",
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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508 default = DEFAULT_MZDECIMAL,
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509 action = "store",
1
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510 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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diff changeset
511 "[default %default]",
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diff changeset
512 "Number of decimal to write for MZ"
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513 ),
0
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514 metavar = "number"
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515 )
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516 parser <- optparse::add_option(
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517 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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518 c("--r_threshold"),
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519 type = "integer",
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520 default = DEFAULT_R_THRESHOLD,
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521 action = "store",
1
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522 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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523 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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524 "R-Pearson correlation threshold between precursor and fragment",
0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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diff changeset
525 "absolute intensity"
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526 ),
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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527 metavar = "number"
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528 )
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529 parser <- optparse::add_option(
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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530 parser,
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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531 c("--min_number_scan"),
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532 type = "numeric",
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533 action = "store",
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534 default = DEFAULT_MINNUMBERSCAN,
1
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535 help = paste(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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536 "[default %default]",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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537 "Fragments are kept if there are found in a minimum number",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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538 "of min_number_scan scans"
0
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539 ),
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540 metavar = "number"
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diff changeset
541 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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542 return(parser)
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543 }
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544
1
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545 stop_with_status <- function(msg, status) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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546 message(sprintf("Error: %s", msg))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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547 message(sprintf("Error code: %s", status))
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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548 base::quit(status = status)
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549 }
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550
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551 check_args_validity <- function(args) { ## nolint cyclocomp_linter
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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552 sysvars <- Sys.getenv()
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553 sysvarnames <- names(sysvars)
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554 if (length(args$output) == 0 || nchar(args$output[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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555 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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556 "Missing output parameters. Please set it with --output.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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557 MISSING_PARAMETER_ERROR
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558 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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559 }
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560 if (length(args$precursors) == 0 || nchar(args$precursors[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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561 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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562 "Missing precursors parameters. Please set it with --precursors.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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563 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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564 )
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565 }
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566 if (length(args$fragments) == 0 || nchar(args$fragments[1]) == 0) {
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567 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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568 "Missing fragments parameters. Please set it with --fragments.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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diff changeset
569 MISSING_PARAMETER_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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570 )
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571 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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572 if (length(args$compounds) == 0 || nchar(args$compounds[1]) == 0) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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573 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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574 "Missing compounds parameters. Please set it with --compounds.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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575 MISSING_PARAMETER_ERROR
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576 )
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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577 }
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578 if (!file.exists(args$precursors)) {
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579 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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580 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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581 "Precursors file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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582 args$precursors
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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583 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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584 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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585 )
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586 }
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587 if (!file.exists(args$fragments)) {
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588 stop_with_status(
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589 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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590 "Fragments file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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591 args$fragments
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592 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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593 MISSING_INPUT_FILE_ERROR
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594 )
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595 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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596 if (!file.exists(args$compounds)) {
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597 stop_with_status(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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598 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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599 "Compounds file %s does not exist or cannot be accessed.",
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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600 args$compounds
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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601 ),
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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602 MISSING_INPUT_FILE_ERROR
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603 )
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604 }
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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605 if (
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606 "_GALAXY_JOB_HOME_DIR" %in% sysvarnames
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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607 || "_GALAXY_JOB_TMP_DIR" %in% sysvarnames
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608 || "GALAXY_MEMORY_MB" %in% sysvarnames
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609 || "GALAXY_MEMORY_MB_PER_SLOT" %in% sysvarnames
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610 || "GALAXY_SLOTS" %in% sysvarnames
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611 ) {
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612 check_galaxy_args_validity(args)
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613 }
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614 }
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615
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616 check_galaxy_args_validity <- function(args) {
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617 if (!file.exists(args$output)) {
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618 stop_with_status(
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619 sprintf(
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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620 "Output file %s does not exist or cannot be accessed.",
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621 args$output
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622 ),
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623 MISSING_INPUT_FILE_ERROR
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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624 )
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625 }
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626 }
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627
0
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628 main <- function(args) {
1
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629 if (args$version) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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630 cat(sprintf("%s\n", MS2SNOOP_VERSION))
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631 base::quit(status = 0)
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632 }
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633 sessionInfo()
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634 check_args_validity(args)
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635 if (args$debug) {
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636 set_debug()
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637 }
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638 if (args$verbose) {
df2672c37732 planemo upload commit 42359ca78388ce5221bc88905a78c996c758aa43
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639 set_verbose()
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640 }
0
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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641 ## MSpurity precursors file
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642 precursors <- read.table(
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643 file = args$precursors,
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644 header = TRUE,
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645 sep = "\t",
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diff changeset
646 quote = "\""
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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diff changeset
647 )
91a3242fd67f "planemo upload commit c7676a9c7ac542043691d735285ae19e430bf032"
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648 ## MSpurity fragments file
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649 fragments <- read.table(
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650 file = args$fragments,
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651 header = TRUE,
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652 sep = "\t",
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653 quote = "\""
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654 )
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655 ## list of compounds : col1=Name of molecule, col2=m/z, col3=retention time
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656 compounds <- read.table(
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657 file = args$compounds,
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658 sep = "\t",
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659 quote = "\"",
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660 header = TRUE
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661 )
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662
1
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663 res_all <- NULL
0
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664 for (i in seq_len(nrow(compounds))) {
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665 ## loop execution for all compounds in the compounds file
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666 res_cor <- NULL
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667 res_cor <- extract_fragments(
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668 precursors = precursors,
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669 fragments = fragments,
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670 mzref = compounds[[2]][i],
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671 rtref = compounds[[3]][i],
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672 c_name = compounds[[1]][i],
1
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673 min_number_scan = args$min_number_scan,
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674 mzdecimal = args$mzdecimal,
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675 r_threshold = args$r_threshold,
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676 seuil_ra = args$seuil_ra,
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677 tolmz = args$tolmz,
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678 tolrt = args$tolrt
0
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679 )
1
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680 if (!is.null(res_cor)) {
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681 if (is.null(res_all)) {
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682 res_all <- res_cor
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683 } else {
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684 res_all <- rbind(res_all, res_cor)
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685 }
0
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686 }
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687 }
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688
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689 if (is.null(res_all)) {
1
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690 stop_with_status("No result at all!", NO_ANY_RESULT_ERROR)
0
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691 }
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692 write.table(
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693 x = res_all,
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694 file = args$output,
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695 sep = "\t",
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696 row.names = FALSE
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697 )
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698 }
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699
1
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700 unset_debug()
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701 unset_verbose()
0
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702 args <- optparse::parse_args(create_parser())
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703 main(args)
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704
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705 warnings()