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1 #!usr/bin/perl
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2
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3 ### Perl modules
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4 use warnings;
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5 use strict;
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6 use Getopt::Long qw(GetOptions); #Creation of script options
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7 use Pod::Usage qw(pod2usage); #Creation of script options
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8
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9 #Personnal packages
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10 use FindBin ; ## Allows you to locate the directory of original perl script
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11 #use lib $FindBin::Bin;
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12 use lib "$FindBin::Bin/lib";
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13 use IonFiltration;
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14
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15 my ($file, $mass_file, $opt, $dataMatrix, $combined_DMVM, $repres_opt, $rt_threshold, $mass_threshold, $output_sif, $output_tabular, $correl_threshold, $intensity_threshold, $intensity_pourc); #Options to complete
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16
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17 ########################
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18 ### Options and help ###
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19 ########################
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20
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21 GetOptions("f=s"=>\$file, "m=s"=>\$mass_file, "o=s"=>\$opt, "d=s"=>\$dataMatrix, "v=s"=>\$combined_DMVM, "r=s"=>\$repres_opt, "rt=f"=>\$rt_threshold, "mass=f"=>\$mass_threshold, "output_sif=s"=>\$output_sif, "output_tabular=s"=>\$output_tabular, "correl=s"=>\$correl_threshold, "IT=f"=>\$intensity_threshold, "IP=f"=>\$intensity_pourc) or pod2usage(2);
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22
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23 ### Check required parameters :
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24 pod2usage({-message=>q{Mandatory argument '-f' is missing}, -exitval=>1, -verbose=>0}) unless $file;
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25 #pod2usage({-message=>q{Mandatory argument '-m' is missing}, -exitval=>1, -verbose=>0}) unless $mass_file;
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26 pod2usage({-message=>q{Mandatory argument '-o' is missing. It correspond to the grouping method for analytical correlation groups formation.
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27 #It should be a number (1 ; 2 or 3) :
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28 # 1 : Don't take into acount mass information (only RT) ;
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29 # 2 : Check that all mass differences are include in a specific list and taking into acount RT information
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30 # 3 : Check that all mass differences are include in a specific list, ignoring RT information
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31 #To use the tool without takinf into account mass and RT information, use option 1 and define the RT threshold to 999999999.}, -exitval=>1, -verbose=>0}) unless $opt;
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32 pod2usage({-message=>q{Mandatory argument '-r' is missing. It correspond to the group representent choosing method for analytical correlation groups formation.
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33 It should be one of the 3 options below :
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34 "mass" : choose the ion with the highest mass as the representant
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35 "intensity" : choose the ion with the highest intensity as the representant
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36 "mixt" : choose the ion with the highest (mass^2 * intensity) as the representant
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37 "max_intensity_max_mass" : choose tha ion witht he highest intenisty among the 5 most intense ions of the group}, -exitval=>1, -verbose=>0}) unless $repres_opt;
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38 pod2usage({-message=>q{Mandatory argument '-d' is missing}, -exitval=>1, -verbose=>0}) unless $dataMatrix;
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39 pod2usage({-message=>q{Mandatory argument '-v' is missing}, -exitval=>1, -verbose=>0}) unless $combined_DMVM;
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40 #pod2usage({-message=>q{Mandatory argument '-rt' is missing}, -exitval=>1, -verbose=>0}) unless $rt_threshold;
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41 #pod2usage({-message=>q{Mandatory argument '-mass' is missing}, -exitval=>1, -verbose=>0}) unless $mass_threshold;
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42 pod2usage({-message=>q{Mandatory argument '-correl' is missing}, -exitval=>1, -verbose=>0}) unless $correl_threshold;
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43 pod2usage({-message=>q{Mandatory argument '-output_tabular' is missing}, -exitval=>1, -verbose=>0}) unless $output_tabular;
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44 pod2usage({-message=>q{Mandatory argument '-output_sif' is missing}, -exitval=>1, -verbose=>0}) unless $output_sif;
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45
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46
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47 #if(($opt != 1) && ($opt != 2) && ($opt != 3)){
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48 # print "you must indicate \"1\", \"2\" or \"3\" for the --o otpion\n";
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49 # exit;
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50 #}
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51
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52
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53
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54 if(($repres_opt ne "mass") && ($repres_opt ne "intensity") && ($repres_opt ne "mixt") && ($repres_opt ne "max_intensity_max_mass")){
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55 print "you must indicate \"mass\", \"intensity\", \"mix\" or \"max_intensity_max_mass\" for the --r otpion\n";
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56 exit;
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57 }
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58
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59
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60
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61 #########################################################################
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62 #### Création of a hash containing all adduits and fragments possible ###
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63 #########################################################################
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64
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65 my %hmass;
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66 if($opt != 1){
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67 %hmass = IonFiltration::MassCollecting($mass_file);
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68
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69 }
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70
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71 my $refhmass = \%hmass;
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72
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73 print "Création of a hash containing all adduits and fragments possible\n";
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74
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75
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76 ########################################################
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77 ### Creation of a sif table + correlation filtration ###
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78 ########################################################
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79
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80 my %hrtmz;
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81 ($output_sif, %hrtmz) = IonFiltration::sifTableCreation($file, $output_sif, $opt, $rt_threshold, $mass_threshold, $correl_threshold, $dataMatrix, $output_tabular, $combined_DMVM, $repres_opt, $intensity_threshold, $intensity_pourc, \%hmass);
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82 print "Creation of a sif table + correlation filtration done\n";
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83
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84
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85 ######################################################
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86 ### Analytic correlation filtrering follow options ###
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87 ######################################################
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88
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89 my %hheader_file;
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90 my %hduplicate;
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91
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92 my %hcorrelgroup;
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93 my $groupct=1;
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94
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95 my $linenb3=0;
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96 my %hheader_line;
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97
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98
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99
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100 open (F1, $output_sif) or die "Impossible to open $output_sif\n";
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101
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102 while(my $line = <F1>){
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103 my $count=0;
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104 chomp $line;
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105 my @tline = split(/\t/, $line);
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106 my $a = $tline[0];
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107 my $b = $tline[2];
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108
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109 my $amass=$hrtmz{$a}{mz};
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110 my $atemp=$hrtmz{$a}{rt};
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111 my $bmass= $hrtmz{$b}{mz};
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112 my $btemp=$hrtmz{$b}{rt};
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113 my $diff = $amass-$bmass;
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114 $diff = abs($diff);
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115
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116 ### Option 1: Don't take into acount mass information ###
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117
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118 if($opt == 1){
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119 my $btplus = $btemp + $rt_threshold;
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120 my $btmoins = $btemp - $rt_threshold;
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121 if(($btmoins <= $atemp) && ($atemp <= $btplus)){
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122 foreach my $k (keys %hcorrelgroup){
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123 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){
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124 $hcorrelgroup{$k}{$a}=1;
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125 $hcorrelgroup{$k}{$b}=1;
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126 $count++;
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127 last;
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128 }
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129 }
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130 if($count == 0){
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131 my $groupnb="group".$groupct;
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132 $hcorrelgroup{$groupnb}{$a}=1;
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133 $hcorrelgroup{$groupnb}{$b}=1;
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134 $groupct ++;
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135 }
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136 }
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137 }
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138
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139
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140
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141 ### Option 2: Check that all mass differences are include in a specific list taking into account RT information ###
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142
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143 elsif($opt == 2){
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144
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145 my $print = 0;
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146 foreach my $s (keys %{$refhmass}){
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147 foreach my $r (keys %{$refhmass->{$s}}){
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148 my $rm = $r - $mass_threshold;
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149 my $rp = $r + $mass_threshold;
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150 if(($diff <= $rp) && ($diff >= $rm)){
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151 if($print == 0){
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152 my $btplus = $btemp + $rt_threshold;
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153 my $btmoins = $btemp - $rt_threshold;
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154
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155 if(($btmoins <= $atemp) && ($atemp <= $btplus)){
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156 foreach my $k (keys %hcorrelgroup){
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157 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){
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158 $hcorrelgroup{$k}{$a}=1;
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159 $hcorrelgroup{$k}{$b}=1;
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160 $count++;
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161 last;
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162 }
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163 }
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164 if($count == 0){
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165 my $groupnb="group".$groupct;
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166 $hcorrelgroup{$groupnb}{$a}=1;
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167 $hcorrelgroup{$groupnb}{$b}=1;
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168 $groupct ++;
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169 }
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170 $print = 1;
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171 }
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172 }
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173 }
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174 }
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175 }
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176 }
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177
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178
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179 ### Option 3: Check that all mass differences are include in a specific list, ignoring RT information ###
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180
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181 elsif($opt == 3){
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182
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183 my $print = 0;
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184 foreach my $s (keys %{$refhmass}){
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185 foreach my $r (keys %{$refhmass->{$s}}){
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186 my $rm = $r - $mass_threshold;
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187 my $rp = $r + $mass_threshold;
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188 if(($diff <= $rp) && ($diff >= $rm)){
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189 if($print == 0){
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190
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191 foreach my $k (keys %hcorrelgroup){
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192 if((defined($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 $print = 1;
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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 }
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211 }
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212 close F1;
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213
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214 print "Analytic correlation filtrering follow options done\n";
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215
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216
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217 #############################################
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218 ### Join groups that have been subdivided ###
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219 #############################################
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220
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221 my @tdelete;
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222
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223 foreach my $k (keys %hcorrelgroup){
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224 foreach my $i (keys %{$hcorrelgroup{$k}}){
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225 foreach my $v (keys %hcorrelgroup){
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226 my $count = 0;
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227 if ($v ne $k){
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228 foreach my $w (keys %{$hcorrelgroup{$v}}){
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229 if($w eq $i){
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230 $count = 1;
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231 push(@tdelete, $v);
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232 }
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233 }
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234 }
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235 if($count == 1){
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236 foreach my $w (keys %{$hcorrelgroup{$v}}){
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237 $hcorrelgroup{$k}{$w}=$hcorrelgroup{$v}{$w};
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238 }
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239 delete($hcorrelgroup{$v});
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240 }
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241 }
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242 }
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243 }
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244
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245 foreach my $t (@tdelete){
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246 delete($hcorrelgroup{$t});
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247 }
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248
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249
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250 ### Do it twice to see if it fix the problem of unmerge groups
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251
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252 foreach my $k (keys %hcorrelgroup){
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253 foreach my $i (keys %{$hcorrelgroup{$k}}){
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254 foreach my $v (keys %hcorrelgroup){
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255 my $count = 0;
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256 if ($v ne $k){
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257 foreach my $w (keys %{$hcorrelgroup{$v}}){
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258 if($w eq $i){
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259 $count = 1;
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260 push(@tdelete, $v);
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261 }
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262 }
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263 }
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264 if($count == 1){
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265 foreach my $w (keys %{$hcorrelgroup{$v}}){
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266 $hcorrelgroup{$k}{$w}=$hcorrelgroup{$v}{$w};
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267 }
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268 delete($hcorrelgroup{$v});
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269 }
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270 }
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271 }
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272 }
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273
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274 foreach my $t (@tdelete){
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275 delete($hcorrelgroup{$t});
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276 }
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277
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278 print "Join groups that have been subdivided done\n";
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279
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280 #######################################################
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281 ### Addition of annotation information among groups ###
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282 #######################################################
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283
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284 foreach my $k (keys %hcorrelgroup){
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285 foreach my $i (keys %{$hcorrelgroup{$k}}){
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286 foreach my $j (keys %{$hcorrelgroup{$k}}){
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287 my $count = 0;
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288 if ($i ne $j){
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289
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290 my $a = $hrtmz{$i}{mz};
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291 my $b = $hrtmz{$j}{mz};
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292
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293 my $diff = $a - $b;
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294 my $sign;
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295 if($diff>0){
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296 $sign="+";
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297 }
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298 if($diff<0){
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299 $sign="-";
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300 }
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301 $diff = abs($diff);
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302
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303 foreach my $z (keys %{$refhmass}){
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304
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305 foreach my $y (keys %{$refhmass->{$z}}){
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306 my $ym = $y - $mass_threshold;
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307 my $yp = $y + $mass_threshold;
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308
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309
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310 if(($diff <= $yp) && ($diff >= $ym)){
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311 my $diff_list = $diff - $y;
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312 $diff_list = abs($diff_list);
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313 $diff_list = sprintf ("%0.6f", $diff_list);
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314
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315 if($hcorrelgroup{$k}{$i} eq 1){
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316 my $val = "@".$j."|".$sign."(".$z.")(".$diff_list.")|";
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317 $hcorrelgroup{$k}{$i}=$val;
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318 $count ++;
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319 }
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320 else{
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321 if($count == 0){
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322 my $val = "@".$j."|".$sign."(".$z.")(".$diff_list.")|";
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323 $hcorrelgroup{$k}{$i}.=$val;
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324 $count ++;
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325 }
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326 else{
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327 my $val = $sign."(".$z.")(".$diff_list.")|";
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328 $hcorrelgroup{$k}{$i}.=$val;
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329 $count ++;
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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 }
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336 }
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337 }
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338 }
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339
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340
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341 print "Addition of annotation information among groups done\n";
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342
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343
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344 ####################################################
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345 ### Choose the representative ion for each group ###
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346 ####################################################
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347
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348 my %hgrouprepres;
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349
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350 open(F3, $dataMatrix);
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351
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352 while (my $line = <F3>){
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353 chomp $line;
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354
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355 my @tline = split (/\t/, $line);
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356
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357 foreach my $k (keys %hcorrelgroup){
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358 foreach my $i (keys %{$hcorrelgroup{$k}}){
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359 if($tline[0] eq $i){
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360 $hgrouprepres{$k}{$i}{mass}=$hrtmz{$tline[0]}{mz};
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361 my $intensity;
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362 my $nbsubjects=0;
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363 for(my $y=1;$y<scalar(@tline);$y++){
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364 $intensity += $tline[$y];
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365 $nbsubjects ++;
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366 }
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367 my $meanintensity = $intensity/$nbsubjects;
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368 $hgrouprepres{$k}{$i}{intensity}=$meanintensity;
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369 $hgrouprepres{$k}{$i}{squaredmassint}=($hgrouprepres{$k}{$i}{mass}**2)/($hgrouprepres{$k}{$i}{intensity});
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370 }
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371 }
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372 }
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373 }
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374 close F3;
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375
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376 foreach my $z (keys %hgrouprepres){
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377 my $max_intensity = 0;
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378 my $max_int_ion = "";
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379 my $max_mass = 0;
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380 my $max_mass_ion = "";
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381 my $max_squared = 0;
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382 my $max_squared_ion = "";
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383 foreach my $w (keys %{$hgrouprepres{$z}}){
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384 if($hgrouprepres{$z}{$w}{intensity} > $max_intensity){
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385 $max_intensity = $hgrouprepres{$z}{$w}{intensity};
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386 $max_int_ion = $w;
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387 }
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388 if($hgrouprepres{$z}{$w}{mass} > $max_mass){
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389 $max_mass = $hgrouprepres{$z}{$w}{mass};
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390 $max_mass_ion = $w;
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391 }
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392 if($hgrouprepres{$z}{$w}{squaredmassint} > $max_squared){
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393 $max_squared = $hgrouprepres{$z}{$w}{squaredmassint};
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394 $max_squared_ion = $w;
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395 }
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396 }
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397
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398 my $max_int_max_mass_ion="";
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399
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400 if($repres_opt eq "max_intensity_max_mass"){
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401 my %hfirst;
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402 my $first=0;
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403 foreach my $w (reverse sort {$hgrouprepres{$z}{$a}{intensity} <=> $hgrouprepres{$z}{$b}{intensity} } keys %{$hgrouprepres{$z}}){
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404 $first ++;
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405 if ($first <= 3){
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406 $hfirst{$w} = $hgrouprepres{$z}{$w}{intensity};
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407 }
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408 }
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409
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410 my $first_2 = 0;
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411 my $intens_max = 0;
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412 my $mass_max = 0;
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413
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414 foreach my $y (reverse sort {$hfirst{$a} <=> $hfirst{$b}} keys %hfirst){
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415
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416 $first_2 ++;
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417 if($first_2 == 1){
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418 $intens_max = $hfirst{$y};
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419 if($intensity_threshold > $intens_max){
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420 $intensity_threshold = 0;
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421 }
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422 $max_int_max_mass_ion = $y;
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423 $mass_max = $hgrouprepres{$z}{$y}{mass};
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424 }
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425 if($hgrouprepres{$z}{$y}{mass} > $mass_max){
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426 if($hfirst{$y}>$intensity_threshold){
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427 my $a = $intens_max * $intensity_pourc;
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428 if($hfirst{$y} > $a){
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429 $max_int_max_mass_ion = $y;
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430 $mass_max = $hgrouprepres{$z}{$y}{mass};
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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 }
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436
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437 $hgrouprepres{$z}{max_int}=$max_int_ion;
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438 $hgrouprepres{$z}{max_mass}=$max_mass_ion;
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439 $hgrouprepres{$z}{max_squared}=$max_squared_ion;
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440 $hgrouprepres{$z}{max_int_max_mass}=$max_int_max_mass_ion;
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441
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442 }
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443
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444
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445 print "Choose the representative ion for each group done\n";
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446
|
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447 #############################################################################
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448 ### Addition of annotation information relative to the representative ion ###
|
|
|
449 #############################################################################
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450
|
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451 my %hreprescomparison;
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452
|
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453 my $representative="";
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454
|
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455 if($opt != 1){
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456 foreach my $k (keys %hcorrelgroup){
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457 foreach my $i (keys %{$hcorrelgroup{$k}}){
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458
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459 if($repres_opt eq "mass"){$representative = $hgrouprepres{$k}{max_mass}}
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|
460 if($repres_opt eq "intensity"){$representative = $hgrouprepres{$k}{max_int}}
|
|
|
461 if($repres_opt eq "mixt"){$representative = $hgrouprepres{$k}{max_squared}}
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|
462 if($repres_opt eq "max_intensity_max_mass"){$representative = $hgrouprepres{$k}{max_int_max_mass}}
|
|
|
463
|
|
|
464
|
|
|
465 my $count = 0;
|
|
|
466 if ($i ne $representative){
|
|
|
467
|
|
|
468 my $a = $hrtmz{$i}{mz};
|
|
|
469 my $b = $hrtmz{$representative}{mz};
|
|
|
470
|
|
|
471 my $diff = $a - $b;
|
|
|
472 my $sign;
|
|
|
473 if($diff>0){
|
|
|
474 $sign="+";
|
|
|
475 }
|
|
|
476 if($diff<0){
|
|
|
477 $sign="-";
|
|
|
478 }
|
|
|
479 $diff = abs($diff);
|
|
|
480
|
|
|
481 foreach my $z (keys %{$refhmass}){
|
|
|
482
|
|
|
483 foreach my $y (keys %{$refhmass->{$z}}){
|
|
|
484 my $ym = $y - $mass_threshold;
|
|
|
485 my $yp = $y + $mass_threshold;
|
|
|
486
|
|
|
487 if(($diff <= $yp) && ($diff >= $ym)){
|
|
|
488 my $diff_list = $diff - $y;
|
|
|
489 $diff_list = abs($diff_list);
|
|
|
490 $diff_list = sprintf ("%0.4f", $diff_list);
|
|
|
491 if($hcorrelgroup{$k}{$i} eq 1){
|
|
|
492 my $valrep = "[M ".$sign."(".$z.")]|";
|
|
|
493 $hreprescomparison{$k}{$i}{repres_diff}=$valrep;
|
|
|
494 $count ++;
|
|
|
495 }
|
|
|
496 else{
|
|
|
497 if($count == 0){
|
|
|
498 my $valrep = "[M ".$sign."(".$z.")]|";
|
|
|
499 $hreprescomparison{$k}{$i}{repres_diff}.=$valrep;
|
|
|
500 $count ++;
|
|
|
501 }
|
|
|
502 else{
|
|
|
503 my $valrep = "[M ".$sign."(".$z.")]|";
|
|
|
504 $hreprescomparison{$k}{$i}{repres_diff}.=$valrep;
|
|
|
505 $count ++;
|
|
|
506 }
|
|
|
507 }
|
|
|
508 }
|
|
|
509 }
|
|
|
510 }
|
|
|
511 }
|
|
|
512 else{
|
|
|
513 $hreprescomparison{$k}{$i}{repres_diff}="M";
|
|
|
514 }
|
|
|
515 }
|
|
|
516 }
|
|
|
517 }
|
|
|
518
|
|
|
519
|
|
|
520 print "Addition of annotation information relative to the representative ion done\n";
|
|
|
521
|
|
|
522 ##############################
|
|
|
523 ### Print in result file ! ###
|
|
|
524 ##############################
|
|
|
525
|
|
|
526 open(F4, ">$output_tabular");
|
|
|
527 open(F5, $combined_DMVM);
|
|
|
528
|
|
|
529 my $line_nb = 0;
|
|
|
530 my %hheader;
|
|
|
531 while (my $line = <F5>){
|
|
|
532 chomp $line;
|
|
|
533
|
|
|
534
|
|
|
535 my @tline = split (/\t/, $line);
|
|
|
536
|
|
|
537 if($line_nb == 0){
|
|
|
538 print F4 "$line\tACorF_groups";
|
|
|
539 if($opt == 1){
|
|
|
540 if($repres_opt eq "intensity"){print F4 "\tACorF_filter\tintensity_repres\n"}
|
|
|
541 if($repres_opt eq "mass"){print F4 "\tACorF_filter\tmass_repres\n"}
|
|
|
542 if($repres_opt eq "mixt"){print F4 "\tACorF_filter\tmass2intens_repres\n"}
|
|
|
543 if($repres_opt eq "max_intensity_max_mass"){print F4 "\tACorF_filter\tmax_intensity_max_mass_repres\n"}
|
|
|
544 }
|
|
|
545 else{
|
|
|
546 if($repres_opt eq "intensity"){print F4 "\tisotopes_adducts_fragments_[\@id|annotation(delta_annotation)]\tACorF_filter\tintensity_repres\tannotation_relative_to_representative\n"}
|
|
|
547 if($repres_opt eq "mass"){print F4 "\tisotopes_adducts_fragments_[\@id|annotation(delta_annotation)]\tACorF_filter\tmass_repres\tannotation_relative_to_representative\n"}
|
|
|
548 if($repres_opt eq "mixt"){print F4 "\tisotopes_adducts_fragments_[\@id|annotation(delta_annotation)]\tACorF_filter\tmass2intens_repres\tannotation_relative_to_representative\n"}
|
|
|
549 if($repres_opt eq "max_intensity_max_mass"){print F4 "\tisotopes_adducts_fragments_[\@id|annotation(delta_annotation)]\tACorF_filter\tmax_intensity_max_mass_repres\tannotation_relative_to_representative\n"}
|
|
|
550 }
|
|
|
551
|
|
|
552
|
|
|
553 ### Creation of a header hash
|
|
|
554 for(my $i=0; $i<scalar(@tline);$i++){
|
|
|
555 my $a = $tline[$i];
|
|
|
556 $hheader{$a}=$i;
|
|
|
557 }
|
|
|
558 }
|
|
|
559
|
|
|
560 else{
|
|
|
561 my $find = 0;
|
|
|
562 foreach my $v (keys %hcorrelgroup){
|
|
|
563 if(defined($hgrouprepres{$v}{$tline[0]})){
|
|
|
564 print F4 "$line\t$v";
|
|
|
565
|
|
|
566 if($opt != 1){
|
|
|
567 if(defined($hcorrelgroup{$v}{$tline[0]})){
|
|
|
568 print F4 "\t$hcorrelgroup{$v}{$tline[0]}\t";
|
|
|
569
|
|
|
570 }
|
|
|
571 else{
|
|
|
572 print F4 "\t";
|
|
|
573 }
|
|
|
574 }
|
|
|
575 else{
|
|
|
576 print F4 "\t";
|
|
|
577 }
|
|
|
578
|
|
|
579 if($repres_opt eq "intensity"){
|
|
|
580 if($tline[0] eq $hgrouprepres{$v}{max_int}){
|
|
|
581 print F4 "1\t";
|
|
|
582 }
|
|
|
583 else{
|
|
|
584 print F4 "0\t";
|
|
|
585 }
|
|
|
586 $find = 1;
|
|
|
587 }
|
|
|
588 if($repres_opt eq "mass"){
|
|
|
589 if($tline[0] eq $hgrouprepres{$v}{max_mass}){
|
|
|
590 print F4 "1\t";
|
|
|
591 }
|
|
|
592 else{
|
|
|
593 print F4 "0\t";
|
|
|
594 }
|
|
|
595 $find = 1;
|
|
|
596 }
|
|
|
597 if($repres_opt eq "mixt"){
|
|
|
598 if($tline[0] eq $hgrouprepres{$v}{max_squared}){
|
|
|
599 print F4 "1\t";
|
|
|
600 }
|
|
|
601 else{
|
|
|
602 print F4 "0\t";
|
|
|
603 }
|
|
|
604 $find = 1;
|
|
|
605 }
|
|
|
606 if($repres_opt eq "max_intensity_max_mass"){
|
|
|
607 if($tline[0] eq $hgrouprepres{$v}{max_int_max_mass}){
|
|
|
608 print F4 "1\t";
|
|
|
609 }
|
|
|
610 else{
|
|
|
611 print F4 "0\t";
|
|
|
612 }
|
|
|
613 $find = 1;
|
|
|
614 }
|
|
|
615
|
|
|
616 if($repres_opt eq "intensity"){print F4 "$hgrouprepres{$v}{max_int}\t"}
|
|
|
617 if($repres_opt eq "mass"){print F4 "$hgrouprepres{$v}{max_mass}\t"}
|
|
|
618 if($repres_opt eq "mixt"){print F4 "$hgrouprepres{$v}{max_squared}\t"}
|
|
|
619 if($repres_opt eq "max_intensity_max_mass"){print F4 "$hgrouprepres{$v}{max_int_max_mass}\t"}
|
|
|
620
|
|
|
621 if($opt != 1){
|
|
|
622 if(defined($hreprescomparison{$v}{$tline[0]}{repres_diff})){
|
|
|
623 print F4 "$hreprescomparison{$v}{$tline[0]}{repres_diff}\n";
|
|
|
624 }
|
|
|
625 else{
|
|
|
626 print F4 "-\n";
|
|
|
627 }
|
|
|
628 }
|
|
|
629 else{
|
|
|
630 print F4 "\n";
|
|
|
631 }
|
|
|
632 }
|
|
|
633 }
|
|
|
634 if($find == 0){
|
|
|
635 $groupct ++;
|
|
|
636 my $group = "group".$groupct;
|
|
|
637 if($opt != 1){
|
|
|
638 print F4 "$line\t$group\t-\t-\t-\t-\n";
|
|
|
639 }
|
|
|
640 else{
|
|
|
641 print F4 "$line\t$group\t-\t-\n";
|
|
|
642 }
|
|
|
643 }
|
|
|
644 }
|
|
|
645 $line_nb ++;
|
|
|
646 }
|
|
|
647
|
|
|
648 print "Print in result file done\n";
|
|
|
649
|
|
|
650 print "All steps done\n";
|
|
|
651
|
