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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 "The mass difference already exists : $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 return %hmass;
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36
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37 }
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38
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39
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40
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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 ### Creation of a sif table + correlation filtration ###
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47 ########################################################
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48
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49
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50 sub sifTableCreation{
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51
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52 my $file = $_[0];
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53 my $output_sif = $_[1];
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54 # my $opt = $_[2];
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55 # my $rt_threshold = $_[3];
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56 # my $mass_threshold = $_[4];
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57 my $correl_threshold = $_[5];
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58 # my $dataMatrix = $_[6];
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59 # my $output_tabular = $_[7];
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60 my $combined_DMVM = $_[8];
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61 # my $repres_opt = $_[9];
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62 # my $intensity_threshold = $_[10];
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63 # my $intensity_pourc = $_[11];
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64 # my $refhmass = $_[12];
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65
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66
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67
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68
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69 my %hheader_file;
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70 my %hduplicate;
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71
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72 my %hcorrelgroup;
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73 my $groupct=1;
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74
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75
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76 my $linenb3=0;
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77 my %hheader_line;
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78 my %hrtmz;
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79
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80 open (F5, $combined_DMVM);
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81 while(my $line = <F5>){
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82 chomp $line;
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83 my @tline = split(/\t/, $line);
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84
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85 if($linenb3 == 0){
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86 for(my $i=0; $i<scalar(@tline);$i++){
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87 my $a = $tline[$i];
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88 $hheader_line{$a}=$i;
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89 }
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90 }
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91 else{
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92 if(defined($hheader_line{mzmed})){
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93 my $b = $tline[$hheader_line{mzmed}];
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94 $hrtmz{$tline[0]}{mz}=$b;
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95 }
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96 else{
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97 my $b = $tline[$hheader_line{mz}];
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98 $hrtmz{$tline[0]}{mz}=$b;
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99 }
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100 if(defined($hheader_line{rtmed})){
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101 my $d = $tline[$hheader_line{rtmed}];
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102 $hrtmz{$tline[0]}{rt}=$d;
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103 }
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104 else{
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105 my $d = $tline[$hheader_line{rt}];
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106 $hrtmz{$tline[0]}{rt}=$d;
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107 }
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108 }
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109
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110 $linenb3 ++;
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111 }
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112 close F5;
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113
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114
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115 my $linenb=0;
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116
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117 open (F1, $file) or die "Impossible to open $file\n";
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118 open(F2, ">$output_sif") or die "Impossible to open $output_sif\n";
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119
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120
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121 while(my $line = <F1>){
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122 chomp $line;
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123 my @tline = split(/\t/, $line);
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124
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125 ###############################
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126 ### Création of a sif table ###
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127 ###############################
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128
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129 if($linenb == 0){
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130 for(my $i=0; $i<scalar(@tline);$i++){
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131 my $a = $tline[$i];
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132 $hheader_file{$i}=$a;
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133 }
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134 }
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135 else{
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136 for(my $i=1; $i<scalar(@tline);$i++){
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137 my $a=$tline[0];
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138 my $b=$hheader_file{$i};
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139 my $coef=$tline[$i];
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140
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141 if($a eq $b){
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142 # print "This is a correlation between A ($a) and A ($b) !\n"
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143 }
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144 else{
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145
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146 #########################
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147 ### Remove duplicates ###
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148 #########################
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149
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150 my $y = $a."/".$b;
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151 my $z = $b."/".$a;
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152
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153 if((!(defined($hduplicate{$y}))) && (!(defined($hduplicate{$z})))){
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154
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155 $hduplicate{$y}=1;
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156 # my $abcoef=abs($coef); # Only when you want to consider negative correlations
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157
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158 # if($abcoef > $correl_threshold){ # Only when you want to consider negative correlations
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159 if($coef > $correl_threshold){
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160
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161 print F2 "$a\t$coef\t$b\n";
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162
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163 my $count=0;
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164
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165 }
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166 }
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167 }
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168 }
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169 }
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170 $linenb ++;
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171 }
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172 close F1;
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173 close F2;
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174 return ($output_sif, %hrtmz);
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175 }
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176
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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 1; |
