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1 #!usr/bin/perl
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2 package IonFiltration;
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3
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4 ### Perl modules
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5 use strict;
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6 use warnings;
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7
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8
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9
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10
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11
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12
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13 ########################################################################
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14 ### Création of a hash containing all adduits and fragments possible ###
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15 ########################################################################
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16
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17
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18 sub MassCollecting{
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19
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20 my $mass_file = $_[0];
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21 my %hmass;
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22
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23 open (F1, $mass_file);
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24
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25 while(my $line = <F1>){
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26 chomp $line;
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27 my @tline = split(/[\t;]/, $line);
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28 if(defined($hmass{$tline[2]})){
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29 print "Il existe déjà une même différence de masse : $tline[2] !\n";
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30 }
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31 $hmass{$tline[1]}{$tline[2]}=$tline[0];
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32 }
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33
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34 close F1;
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35 # my $count=0;
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36 # foreach my $k (keys %hmass){
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37 # $count++;
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38 # }
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39
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40 return %hmass;
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41
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42
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43 }
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44
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45
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46
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47
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48
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49
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50
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51 ########################################################
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52 ### Creation of a sif table + correlation filtration ###
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53 ########################################################
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54
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55
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56 sub sifTableCreation{
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57
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58 my $file = $_[0];
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59 my $output_sif = $_[1];
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60 my $opt = $_[2];
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61 my $rt_threshold = $_[3];
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62 my $mass_threshold = $_[4];
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63 my $correl_threshold = $_[5];
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64 my $dataMatrix = $_[6];
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65 my $output_tabular = $_[7];
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66 my $combined_DMVM = $_[8];
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67 my $repres_opt = $_[9];
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68 my $intensity_threshold = $_[10];
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69 my $intensity_pourc = $_[11];
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70 my $refhmass = $_[12];
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71
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72
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73
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74
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75 my %hheader_file;
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76 my %hduplicate;
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77
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78 my %hcorrelgroup;
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79 my $groupct=1;
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80
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81
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82 my $linenb3=0;
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83 my %hheader_line;
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84 my %hrtmz;
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85
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86 open (F5, $combined_DMVM);
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87 while(my $line = <F5>){
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88 chomp $line;
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89 my @tline = split(/\t/, $line);
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90
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91 if($linenb3 == 0){
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92 for(my $i=0; $i<scalar(@tline);$i++){
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93 my $a = $tline[$i];
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94 $hheader_line{$a}=$i;
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95 }
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96 }
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97 else{
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98 if(defined($hheader_line{mzmed})){
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99 my $b = $tline[$hheader_line{mzmed}];
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100 $hrtmz{$tline[0]}{mz}=$b;
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101 }
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102 else{
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103 my $b = $tline[$hheader_line{mz}];
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104 $hrtmz{$tline[0]}{mz}=$b;
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105 }
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106 if(defined($hheader_line{rtmed})){
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107 my $d = $tline[$hheader_line{rtmed}];
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108 $hrtmz{$tline[0]}{rt}=$d;
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109 }
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110 else{
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111 my $d = $tline[$hheader_line{rt}];
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112 $hrtmz{$tline[0]}{rt}=$d;
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113 }
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114 }
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115
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116 $linenb3 ++;
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117 }
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118 close F5;
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119
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120
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121 my $linenb=0;
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122
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123 open (F1, $file) or die "Impossible to open $file\n";
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124 open(F2, ">$output_sif") or die "Impossible to open $output_sif\n";
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125
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126 while(my $line = <F1>){
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127 chomp $line;
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128 my @tline = split(/\t/, $line);
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129
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130
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131 ###############################
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132 ### Création of a sif table ###
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133 ###############################
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134
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135 if($linenb == 0){
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136 for(my $i=0; $i<scalar(@tline);$i++){
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137 my $a = $tline[$i];
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138 $hheader_file{$i}=$a;
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139 }
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140 }
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141 else{
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142 for(my $i=1; $i<scalar(@tline);$i++){
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143 my $a=$tline[0];
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144 my $b=$hheader_file{$i};
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145 my $coef=$tline[$i];
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146
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147
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148 if($a eq $b){
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149 # print "This is a correlation between A ($a) and A ($b) !\n"
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150 }
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151 else{
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152
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153
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154 #########################
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155 ### Remove duplicates ###
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156 #########################
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157
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158 my $y = $a."/".$b;
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159 my $z = $b."/".$a;
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160
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161 if((!(defined($hduplicate{$y}))) && (!(defined($hduplicate{$z})))){
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162
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163 $hduplicate{$y}=1;
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164
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165 if($coef > $correl_threshold){
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166
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167 print F2 "$a\t$coef\t$b\n";
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168
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169 my $count=0;
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170
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171 ######################################################
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172 ### Analytic correlation filtrering follow options ###
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173 ######################################################
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174
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175
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176
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177 my $amass=$hrtmz{$a}{mz};
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178 my $atemp=$hrtmz{$a}{rt};
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179 my $bmass= $hrtmz{$b}{mz};
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180 my $btemp=$hrtmz{$b}{rt};
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181 my $diff = $amass-$bmass;
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182 $diff = abs($diff);
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183
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184 ### Option 1: Don't take into acount mass information ###
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185
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186 if($opt == 1){
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187 my $btplus = $btemp + $rt_threshold;
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188 my $btmoins = $btemp - $rt_threshold;
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189 if(($btmoins <= $atemp) && ($atemp <= $btplus)){
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190 foreach my $k (keys %hcorrelgroup){
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191
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192 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){
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193 $hcorrelgroup{$k}{$a}=1;
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194 $hcorrelgroup{$k}{$b}=1;
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195 $count++;
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196 last;
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197 }
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198 }
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199 if($count == 0){
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200 my $groupnb="group".$groupct;
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201 $hcorrelgroup{$groupnb}{$a}=1;
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202 $hcorrelgroup{$groupnb}{$b}=1;
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203 $groupct ++;
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204 }
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205
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206 }
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207 }
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208
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209
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210 ### Option 2: Check that all mass differences are include in a specific list taking into account RT information ###
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211
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212 elsif($opt == 2){
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213
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214 my $print = 0;
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215 foreach my $s (keys %{$refhmass}){
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216 foreach my $r (keys %{$refhmass->{$s}}){
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217 my $rm = $r - $mass_threshold;
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218 my $rp = $r + $mass_threshold;
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219 if(($diff <= $rp) && ($diff >= $rm)){
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220 if($print == 0){
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221 my $btplus = $btemp + $rt_threshold;
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222 my $btmoins = $btemp - $rt_threshold;
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223
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224 if(($btmoins <= $atemp) && ($atemp <= $btplus)){
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225 # foreach my $s (keys %{%$refhmass{$r}}){
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226 # print F2 "$line\t$hmass{$r}{$s} : $s ($r)\n";
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227 foreach my $k (keys %hcorrelgroup){
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228 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){
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229 $hcorrelgroup{$k}{$a}=1;
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230 $hcorrelgroup{$k}{$b}=1;
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231 # $hcorrelgroup{$k}{frag}.="#".$s;
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232 $count++;
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233 last;
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234 }
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235 }
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236 if($count == 0){
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237 my $groupnb="group".$groupct;
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238 $hcorrelgroup{$groupnb}{$a}=1;
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239 $hcorrelgroup{$groupnb}{$b}=1;
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240 # $hcorrelgroup{$groupnb}{frag}.="#".$s;
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241 $groupct ++;
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242
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243 }
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244 $print = 1;
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245 }
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246
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247 }
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248 }
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249 }
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250 }
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251 }
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252
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253
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254 ### Option 3: Check that all mass differences are include in a specific list, ignoring RT information ###
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255
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256 elsif($opt == 3){
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257
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258 my $print = 0;
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259 foreach my $s (keys %{$refhmass}){
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260 foreach my $r (keys %{$refhmass->{$s}}){
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261 my $rm = $r - $mass_threshold;
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262 my $rp = $r + $mass_threshold;
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263 if(($diff <= $rp) && ($diff >= $rm)){
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264 if($print == 0){
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265
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266 # foreach my $s (keys %{%$refhmass{$r}}){
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267 # print F2 "$line\t$hmass{$r}{$s} : $s ($r)\n";
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268 foreach my $k (keys %hcorrelgroup){
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269 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){
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270 $hcorrelgroup{$k}{$a}=1;
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271 $hcorrelgroup{$k}{$b}=1;
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272 # $hcorrelgroup{$k}{frag}.="#".$s;
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273 $count++;
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274 last;
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275 }
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276 }
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277 if($count == 0){
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278 my $groupnb="group".$groupct;
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279 $hcorrelgroup{$groupnb}{$a}=1;
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280 $hcorrelgroup{$groupnb}{$b}=1;
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281 # $hcorrelgroup{$groupnb}{frag}.="#".$s;
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282 $groupct ++;
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283 }
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284 $print = 1;
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285 }
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286 }
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287 }
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288 }
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289 }
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290 }
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291
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292
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293 }
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294 }
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295 }
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296 }
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297 $linenb ++;
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298 }
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299 close F1;
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300 close F2;
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301
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302
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303
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304
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305 #############################################
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306 ### Join groups that have been subdivided ###
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307 #############################################
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308
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309 my @tdelete;
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310
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311 foreach my $k (keys %hcorrelgroup){
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312 foreach my $i (keys %{$hcorrelgroup{$k}}){
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313 foreach my $v (keys %hcorrelgroup){
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314 my $count = 0;
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315 if ($v ne $k){
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316 foreach my $w (keys %{$hcorrelgroup{$v}}){
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317 # if($w ne "frag"){
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318 if($w eq $i){
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319 $count = 1;
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320 push(@tdelete, $v);
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321 }
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322 # }
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323 }
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324 }
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325 if($count == 1){
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326 foreach my $w (keys %{$hcorrelgroup{$v}}){
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327 $hcorrelgroup{$k}{$w}=$hcorrelgroup{$v}{$w};
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328 }
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329 delete($hcorrelgroup{$v});
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330 }
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331 }
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332 }
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333 }
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334
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335 foreach my $t (@tdelete){
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336 delete($hcorrelgroup{$t});
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337 }
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338
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339
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340 ### Do it twice to see if it fix the problem of unmerge groups
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341
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342 foreach my $k (keys %hcorrelgroup){
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343 foreach my $i (keys %{$hcorrelgroup{$k}}){
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344 foreach my $v (keys %hcorrelgroup){
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345 my $count = 0;
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346 if ($v ne $k){
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347 foreach my $w (keys %{$hcorrelgroup{$v}}){
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348 # if($w ne "frag"){
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349 if($w eq $i){
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350 $count = 1;
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351 push(@tdelete, $v);
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352 }
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353 # }
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354 }
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355 }
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356 if($count == 1){
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357 foreach my $w (keys %{$hcorrelgroup{$v}}){
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358 $hcorrelgroup{$k}{$w}=$hcorrelgroup{$v}{$w};
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359 }
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360 delete($hcorrelgroup{$v});
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361 }
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362 }
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363 }
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364 }
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365
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366 foreach my $t (@tdelete){
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367 delete($hcorrelgroup{$t});
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368 }
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369
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370
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371
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372 ##########################################
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373 ### Addition of annotation information ###
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374 ##########################################
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375
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376 foreach my $k (keys %hcorrelgroup){
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377 foreach my $i (keys %{$hcorrelgroup{$k}}){
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378 foreach my $j (keys %{$hcorrelgroup{$k}}){
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379 my $count = 0;
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380 if ($i ne $j){
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381
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382 my $a = $hrtmz{$i}{mz};
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383 my $b = $hrtmz{$j}{mz};
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384
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385 my $diff = $a - $b;
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386 my $sign;
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387 if($diff>0){
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388 $sign="+";
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389 }
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390 if($diff<0){
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391 $sign="-";
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392 }
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393 $diff = abs($diff);
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394
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395 foreach my $z (keys %{$refhmass}){
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396
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397 foreach my $y (keys %{$refhmass->{$z}}){
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398 my $ym = $y - $mass_threshold;
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399 my $yp = $y + $mass_threshold;
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400
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401
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402 if(($diff <= $yp) && ($diff >= $ym)){
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403 my $diff_list = $diff - $y;
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404 $diff_list = abs($diff_list);
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405 $diff_list = sprintf ("%0.6f", $diff_list);
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406
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407 if($hcorrelgroup{$k}{$i} eq 1){
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408 my $val = "#".$j."|".$sign."(".$z.")(".$diff_list.")|";
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409 $hcorrelgroup{$k}{$i}=$val;
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410 $count ++;
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411 }
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412 else{
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413 if($count == 0){
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414 my $val = "#".$j."|".$sign."(".$z.")(".$diff_list.")|";
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415 $hcorrelgroup{$k}{$i}.=$val;
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416 $count ++;
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417 }
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418 else{
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419 my $val = $sign."(".$z.")(".$diff_list.")|";
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420 $hcorrelgroup{$k}{$i}.=$val;
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421 $count ++;
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422 }
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423 }
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424 }
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425 }
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426 }
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427 }
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428 }
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429 }
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430 }
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431
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432
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433
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434 ####################################################
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435 ### Choose the representative ion for each group ###
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436 ####################################################
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437
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438 my %hgrouprepres;
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439
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440 open(F3, $dataMatrix);
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441
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442 while (my $line = <F3>){
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443 chomp $line;
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444
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445 my @tline = split (/\t/, $line);
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446
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447
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448
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449 foreach my $k (keys %hcorrelgroup){
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450 foreach my $i (keys %{$hcorrelgroup{$k}}){
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451
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452 if($tline[0] eq $i){
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453 $hgrouprepres{$k}{$i}{mass}=$hrtmz{$tline[0]}{mz};
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454
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455 my $intensity;
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456 my $nbsubjects=0;
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457 for(my $y=1;$y<scalar(@tline);$y++){
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458 $intensity += $tline[$y];
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459 $nbsubjects ++;
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460 }
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461 my $meanintensity = $intensity/$nbsubjects;
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462 $hgrouprepres{$k}{$i}{intensity}=$meanintensity;
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463 $hgrouprepres{$k}{$i}{squaredmassint}=($hgrouprepres{$k}{$i}{mass}**2)/($hgrouprepres{$k}{$i}{intensity});
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464 }
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465 }
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466 }
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467 }
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468 close F3;
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469
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470 foreach my $z (keys %hgrouprepres){
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471 my $max_intensity = 0;
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472 my $max_int_ion = "";
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473 my $max_mass = 0;
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474 my $max_mass_ion = "";
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475 my $max_squared = 0;
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476 my $max_squared_ion = "";
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477 foreach my $w (keys %{$hgrouprepres{$z}}){
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478 if($hgrouprepres{$z}{$w}{intensity} > $max_intensity){
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479 $max_intensity = $hgrouprepres{$z}{$w}{intensity};
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480 $max_int_ion = $w;
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481
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482 }
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483 if($hgrouprepres{$z}{$w}{mass} > $max_mass){
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484 $max_mass = $hgrouprepres{$z}{$w}{mass};
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485 $max_mass_ion = $w;
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486 }
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487 if($hgrouprepres{$z}{$w}{squaredmassint} > $max_squared){
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488 $max_squared = $hgrouprepres{$z}{$w}{squaredmassint};
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489 $max_squared_ion = $w;
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490 }
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491 }
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492
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493 my $max_int_max_mass_ion="";
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494
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495 if($repres_opt eq "max_intensity_max_mass"){
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496 my %hfirst;
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497 my $first=0;
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498 foreach my $w (reverse sort {$hgrouprepres{$z}{$a}{intensity} <=> $hgrouprepres{$z}{$b}{intensity} } keys %{$hgrouprepres{$z}}){
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499 $first ++;
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500 if ($first <= 3){
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501 $hfirst{$w} = $hgrouprepres{$z}{$w}{intensity};
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502 }
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503 }
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|
504
|
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505 my $first_2 = 0;
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|
|
506 my $intens_max = 0;
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|
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507 my $mass_max = 0;
|
|
|
508
|
|
|
509 foreach my $y (reverse sort {$hfirst{$a} <=> $hfirst{$b}} keys %hfirst){
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|
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510
|
|
|
511
|
|
|
512
|
|
|
513 $first_2 ++;
|
|
|
514 if($first_2 == 1){
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|
|
515 $intens_max = $hfirst{$y};
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|
|
516 if($intensity_threshold > $intens_max){
|
|
|
517 $intensity_threshold = 0;
|
|
|
518 }
|
|
|
519 $max_int_max_mass_ion = $y;
|
|
|
520 $mass_max = $hgrouprepres{$z}{$y}{mass};
|
|
|
521 }
|
|
|
522 if($hgrouprepres{$z}{$y}{mass} > $mass_max){
|
|
|
523 if($hfirst{$y}>$intensity_threshold){
|
|
|
524 my $a = $intens_max * $intensity_pourc;
|
|
|
525 if($hfirst{$y} > $a){
|
|
|
526 $max_int_max_mass_ion = $y;
|
|
|
527 $mass_max = $hgrouprepres{$z}{$y}{mass};
|
|
|
528 }
|
|
|
529 }
|
|
|
530 }
|
|
|
531
|
|
|
532 }
|
|
|
533 }
|
|
|
534
|
|
|
535
|
|
|
536 $hgrouprepres{$z}{max_int}=$max_int_ion;
|
|
|
537 $hgrouprepres{$z}{max_mass}=$max_mass_ion;
|
|
|
538 $hgrouprepres{$z}{max_squared}=$max_squared_ion;
|
|
|
539 $hgrouprepres{$z}{max_int_max_mass}=$max_int_max_mass_ion;
|
|
|
540
|
|
|
541 }
|
|
|
542
|
|
|
543
|
|
|
544 ######################
|
|
|
545 ### Print result ! ###
|
|
|
546 ######################
|
|
|
547
|
|
|
548 open(F4, ">$output_tabular");
|
|
|
549 open(F5, $combined_DMVM);
|
|
|
550
|
|
|
551 my $line_nb = 0;
|
|
|
552 my %hheader;
|
|
|
553 while (my $line = <F5>){
|
|
|
554 chomp $line;
|
|
|
555
|
|
|
556
|
|
|
557 my @tline = split (/\t/, $line);
|
|
|
558
|
|
|
559 if($line_nb == 0){
|
|
|
560 print F4 "$line\tACF_groups";
|
|
|
561 if($opt == 1){
|
|
|
562 if($repres_opt eq "intensity"){print F4 "\tintensity_repres\tACF_filter\n"}
|
|
|
563 if($repres_opt eq "mass"){print F4 "\tmass_repres\tACF_filter\n"}
|
|
|
564 if($repres_opt eq "mixt"){print F4 "\tmass2intens_repres\tACF_filter\n"}
|
|
|
565 if($repres_opt eq "max_intensity_max_mass"){print F4 "\tmax_intensity_max_mass_repres\tACF_filter\n"}
|
|
|
566
|
|
|
567 }
|
|
|
568 else{
|
|
|
569 if($repres_opt eq "intensity"){print F4 "\tintensity_repres\tisotopes_adducts_fragments_[#id|annotation(delta_annotation)]\tACF_filter\n"}
|
|
|
570 if($repres_opt eq "mass"){print F4 "\tmass_repres\tisotopes_adducts_fragments_[#id|annotation(delta_annotation)]\tACF_filter\n"}
|
|
|
571 if($repres_opt eq "mixt"){print F4 "\tmass2intens_repres\tisotopes_adducts_fragments_[#id|annotation(delta_annotation)]\tACF_filter\n"}
|
|
|
572 if($repres_opt eq "max_intensity_max_mass"){print F4 "\tmax_intensity_max_mass_repres\tisotopes_adducts_fragments_[#id|annotation(delta_annotation)]\tACF_filter\n"}
|
|
|
573 }
|
|
|
574
|
|
|
575
|
|
|
576 ### Creation of a header hash
|
|
|
577 for(my $i=0; $i<scalar(@tline);$i++){
|
|
|
578 my $a = $tline[$i];
|
|
|
579 $hheader{$a}=$i;
|
|
|
580 }
|
|
|
581 }
|
|
|
582
|
|
|
583 else{
|
|
|
584 my $find = 0;
|
|
|
585 foreach my $v (keys %hcorrelgroup){
|
|
|
586 if(defined($hgrouprepres{$v}{$tline[0]})){
|
|
|
587 print F4 "$line\t$v";
|
|
|
588
|
|
|
589
|
|
|
590 if($repres_opt eq "intensity"){print F4 "\t$hgrouprepres{$v}{max_int}\t"}
|
|
|
591 if($repres_opt eq "mass"){print F4 "\t$hgrouprepres{$v}{max_mass}\t"}
|
|
|
592 if($repres_opt eq "mixt"){print F4 "\t$hgrouprepres{$v}{max_squared}\t"}
|
|
|
593 if($repres_opt eq "max_intensity_max_mass"){print F4 "\t$hgrouprepres{$v}{max_int_max_mass}\t"}
|
|
|
594
|
|
|
595
|
|
|
596 if($opt != 1){
|
|
|
597 if(defined($hcorrelgroup{$v}{$tline[0]})){
|
|
|
598 print F4 "$hcorrelgroup{$v}{$tline[0]}\t";
|
|
|
599 }
|
|
|
600 else{
|
|
|
601 print F4 "\t";
|
|
|
602 }
|
|
|
603 }
|
|
|
604
|
|
|
605 if($repres_opt eq "intensity"){
|
|
|
606 if($tline[0] eq $hgrouprepres{$v}{max_int}){
|
|
|
607 print F4 "conserved\n";
|
|
|
608 }
|
|
|
609 else{
|
|
|
610 print F4 "deleted\n";
|
|
|
611 }
|
|
|
612 $find = 1;
|
|
|
613 }
|
|
|
614 if($repres_opt eq "mass"){
|
|
|
615 if($tline[0] eq $hgrouprepres{$v}{max_mass}){
|
|
|
616 print F4 "conserved\n";
|
|
|
617 }
|
|
|
618 else{
|
|
|
619 print F4 "deleted\n";
|
|
|
620 }
|
|
|
621 $find = 1;
|
|
|
622 }
|
|
|
623 if($repres_opt eq "mixt"){
|
|
|
624 if($tline[0] eq $hgrouprepres{$v}{max_squared}){
|
|
|
625 print F4 "conserved\n";
|
|
|
626 }
|
|
|
627 else{
|
|
|
628 print F4 "deleted\n";
|
|
|
629 }
|
|
|
630 $find = 1;
|
|
|
631 }
|
|
|
632 if($repres_opt eq "max_intensity_max_mass"){
|
|
|
633 if($tline[0] eq $hgrouprepres{$v}{max_int_max_mass}){
|
|
|
634 print F4 "conserved\n";
|
|
|
635 }
|
|
|
636 else{
|
|
|
637 print F4 "deleted\n";
|
|
|
638 }
|
|
|
639 $find = 1;
|
|
|
640 }
|
|
|
641 }
|
|
|
642 }
|
|
|
643 if($find == 0){
|
|
|
644 $groupct ++;
|
|
|
645 my $group = "group".$groupct;
|
|
|
646 if($opt != 1){
|
|
|
647 print F4 "$line\t$group\t-\t-\t-\n";
|
|
|
648 }
|
|
|
649 else{
|
|
|
650 print F4 "$line\t$group\t-\t-\n";
|
|
|
651 }
|
|
|
652 }
|
|
|
653
|
|
|
654
|
|
|
655 }
|
|
|
656
|
|
|
657 $line_nb ++;
|
|
|
658 }
|
|
|
659
|
|
|
660
|
|
|
661 return ($output_sif, $output_tabular);
|
|
|
662 }
|
|
|
663
|
|
|
664
|
|
|
665
|
|
|
666
|
|
|
667
|
|
|
668 1; |
