Mercurial > repos > melpetera > acorf
comparison ACF/Analytic_correlation_filtration.pl @ 0:d03fcbeb0a77 draft
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| author | melpetera |
|---|---|
| date | Fri, 18 Oct 2019 04:59:51 -0400 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:d03fcbeb0a77 |
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| 1 #!usr/bin/perl | |
| 2 | |
| 3 ### Perl modules | |
| 4 use warnings; | |
| 5 use strict; | |
| 6 use Getopt::Long qw(GetOptions); #Creation of script options | |
| 7 use Pod::Usage qw(pod2usage); #Creation of script options | |
| 8 | |
| 9 #Personnal packages | |
| 10 use FindBin ; ## Allows you to locate the directory of original perl script | |
| 11 #use lib $FindBin::Bin; | |
| 12 use lib "$FindBin::Bin/lib"; | |
| 13 use IonFiltration; | |
| 14 | |
| 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 | |
| 16 | |
| 17 ######################## | |
| 18 ### Options and help ### | |
| 19 ######################## | |
| 20 | |
| 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); | |
| 22 | |
| 23 ### Check required parameters : | |
| 24 pod2usage({-message=>q{Mandatory argument '-f' is missing}, -exitval=>1, -verbose=>0}) unless $file; | |
| 25 #pod2usage({-message=>q{Mandatory argument '-m' is missing}, -exitval=>1, -verbose=>0}) unless $mass_file; | |
| 26 pod2usage({-message=>q{Mandatory argument '-o' is missing. It correspond to the grouping method for analytical correlation groups formation. | |
| 27 #It should be a number (1 ; 2 or 3) : | |
| 28 # 1 : Don't take into acount mass information (only RT) ; | |
| 29 # 2 : Check that all mass differences are include in a specific list and taking into acount RT information | |
| 30 # 3 : Check that all mass differences are include in a specific list, ignoring RT information | |
| 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; | |
| 32 pod2usage({-message=>q{Mandatory argument '-r' is missing. It correspond to the group representent choosing method for analytical correlation groups formation. | |
| 33 It should be one of the 3 options below : | |
| 34 "mass" : choose the ion with the highest mass as the representant | |
| 35 "intensity" : choose the ion with the highest intensity as the representant | |
| 36 "mixt" : choose the ion with the highest (mass^2 * intensity) as the representant | |
| 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; | |
| 38 pod2usage({-message=>q{Mandatory argument '-d' is missing}, -exitval=>1, -verbose=>0}) unless $dataMatrix; | |
| 39 pod2usage({-message=>q{Mandatory argument '-v' is missing}, -exitval=>1, -verbose=>0}) unless $combined_DMVM; | |
| 40 #pod2usage({-message=>q{Mandatory argument '-rt' is missing}, -exitval=>1, -verbose=>0}) unless $rt_threshold; | |
| 41 #pod2usage({-message=>q{Mandatory argument '-mass' is missing}, -exitval=>1, -verbose=>0}) unless $mass_threshold; | |
| 42 pod2usage({-message=>q{Mandatory argument '-correl' is missing}, -exitval=>1, -verbose=>0}) unless $correl_threshold; | |
| 43 pod2usage({-message=>q{Mandatory argument '-output_tabular' is missing}, -exitval=>1, -verbose=>0}) unless $output_tabular; | |
| 44 pod2usage({-message=>q{Mandatory argument '-output_sif' is missing}, -exitval=>1, -verbose=>0}) unless $output_sif; | |
| 45 | |
| 46 | |
| 47 #if(($opt != 1) && ($opt != 2) && ($opt != 3)){ | |
| 48 # print "you must indicate \"1\", \"2\" or \"3\" for the --o otpion\n"; | |
| 49 # exit; | |
| 50 #} | |
| 51 | |
| 52 | |
| 53 | |
| 54 if(($repres_opt ne "mass") && ($repres_opt ne "intensity") && ($repres_opt ne "mixt") && ($repres_opt ne "max_intensity_max_mass")){ | |
| 55 print "you must indicate \"mass\", \"intensity\", \"mix\" or \"max_intensity_max_mass\" for the --r otpion\n"; | |
| 56 exit; | |
| 57 } | |
| 58 | |
| 59 | |
| 60 | |
| 61 ######################################################################### | |
| 62 #### Création of a hash containing all adduits and fragments possible ### | |
| 63 ######################################################################### | |
| 64 | |
| 65 my %hmass; | |
| 66 if($opt != 1){ | |
| 67 %hmass = IonFiltration::MassCollecting($mass_file); | |
| 68 | |
| 69 } | |
| 70 | |
| 71 my $refhmass = \%hmass; | |
| 72 | |
| 73 print "Création of a hash containing all adduits and fragments possible\n"; | |
| 74 | |
| 75 | |
| 76 ######################################################## | |
| 77 ### Creation of a sif table + correlation filtration ### | |
| 78 ######################################################## | |
| 79 | |
| 80 my %hrtmz; | |
| 81 ($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); | |
| 82 print "Creation of a sif table + correlation filtration done\n"; | |
| 83 | |
| 84 | |
| 85 ###################################################### | |
| 86 ### Analytic correlation filtrering follow options ### | |
| 87 ###################################################### | |
| 88 | |
| 89 my %hheader_file; | |
| 90 my %hduplicate; | |
| 91 | |
| 92 my %hcorrelgroup; | |
| 93 my $groupct=1; | |
| 94 | |
| 95 my $linenb3=0; | |
| 96 my %hheader_line; | |
| 97 | |
| 98 | |
| 99 | |
| 100 open (F1, $output_sif) or die "Impossible to open $output_sif\n"; | |
| 101 | |
| 102 while(my $line = <F1>){ | |
| 103 my $count=0; | |
| 104 chomp $line; | |
| 105 my @tline = split(/\t/, $line); | |
| 106 my $a = $tline[0]; | |
| 107 my $b = $tline[2]; | |
| 108 | |
| 109 my $amass=$hrtmz{$a}{mz}; | |
| 110 my $atemp=$hrtmz{$a}{rt}; | |
| 111 my $bmass= $hrtmz{$b}{mz}; | |
| 112 my $btemp=$hrtmz{$b}{rt}; | |
| 113 my $diff = $amass-$bmass; | |
| 114 $diff = abs($diff); | |
| 115 | |
| 116 ### Option 1: Don't take into acount mass information ### | |
| 117 | |
| 118 if($opt == 1){ | |
| 119 my $btplus = $btemp + $rt_threshold; | |
| 120 my $btmoins = $btemp - $rt_threshold; | |
| 121 if(($btmoins <= $atemp) && ($atemp <= $btplus)){ | |
| 122 foreach my $k (keys %hcorrelgroup){ | |
| 123 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){ | |
| 124 $hcorrelgroup{$k}{$a}=1; | |
| 125 $hcorrelgroup{$k}{$b}=1; | |
| 126 $count++; | |
| 127 last; | |
| 128 } | |
| 129 } | |
| 130 if($count == 0){ | |
| 131 my $groupnb="group".$groupct; | |
| 132 $hcorrelgroup{$groupnb}{$a}=1; | |
| 133 $hcorrelgroup{$groupnb}{$b}=1; | |
| 134 $groupct ++; | |
| 135 } | |
| 136 } | |
| 137 } | |
| 138 | |
| 139 | |
| 140 | |
| 141 ### Option 2: Check that all mass differences are include in a specific list taking into account RT information ### | |
| 142 | |
| 143 elsif($opt == 2){ | |
| 144 | |
| 145 my $print = 0; | |
| 146 foreach my $s (keys %{$refhmass}){ | |
| 147 foreach my $r (keys %{$refhmass->{$s}}){ | |
| 148 my $rm = $r - $mass_threshold; | |
| 149 my $rp = $r + $mass_threshold; | |
| 150 if(($diff <= $rp) && ($diff >= $rm)){ | |
| 151 if($print == 0){ | |
| 152 my $btplus = $btemp + $rt_threshold; | |
| 153 my $btmoins = $btemp - $rt_threshold; | |
| 154 | |
| 155 if(($btmoins <= $atemp) && ($atemp <= $btplus)){ | |
| 156 foreach my $k (keys %hcorrelgroup){ | |
| 157 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){ | |
| 158 $hcorrelgroup{$k}{$a}=1; | |
| 159 $hcorrelgroup{$k}{$b}=1; | |
| 160 $count++; | |
| 161 last; | |
| 162 } | |
| 163 } | |
| 164 if($count == 0){ | |
| 165 my $groupnb="group".$groupct; | |
| 166 $hcorrelgroup{$groupnb}{$a}=1; | |
| 167 $hcorrelgroup{$groupnb}{$b}=1; | |
| 168 $groupct ++; | |
| 169 } | |
| 170 $print = 1; | |
| 171 } | |
| 172 } | |
| 173 } | |
| 174 } | |
| 175 } | |
| 176 } | |
| 177 | |
| 178 | |
| 179 ### Option 3: Check that all mass differences are include in a specific list, ignoring RT information ### | |
| 180 | |
| 181 elsif($opt == 3){ | |
| 182 | |
| 183 my $print = 0; | |
| 184 foreach my $s (keys %{$refhmass}){ | |
| 185 foreach my $r (keys %{$refhmass->{$s}}){ | |
| 186 my $rm = $r - $mass_threshold; | |
| 187 my $rp = $r + $mass_threshold; | |
| 188 if(($diff <= $rp) && ($diff >= $rm)){ | |
| 189 if($print == 0){ | |
| 190 | |
| 191 foreach my $k (keys %hcorrelgroup){ | |
| 192 if((defined($hcorrelgroup{$k}{$a})) || (defined($hcorrelgroup{$k}{$b}))){ | |
| 193 $hcorrelgroup{$k}{$a}=1; | |
| 194 $hcorrelgroup{$k}{$b}=1; | |
| 195 $count++; | |
| 196 last; | |
| 197 } | |
| 198 } | |
| 199 if($count == 0){ | |
| 200 my $groupnb="group".$groupct; | |
| 201 $hcorrelgroup{$groupnb}{$a}=1; | |
| 202 $hcorrelgroup{$groupnb}{$b}=1; | |
| 203 $groupct ++; | |
| 204 } | |
| 205 $print = 1; | |
| 206 } | |
| 207 } | |
| 208 } | |
| 209 } | |
| 210 } | |
| 211 } | |
| 212 close F1; | |
| 213 | |
| 214 print "Analytic correlation filtrering follow options done\n"; | |
| 215 | |
| 216 | |
| 217 ############################################# | |
| 218 ### Join groups that have been subdivided ### | |
| 219 ############################################# | |
| 220 | |
| 221 my @tdelete; | |
| 222 | |
| 223 foreach my $k (keys %hcorrelgroup){ | |
| 224 foreach my $i (keys %{$hcorrelgroup{$k}}){ | |
| 225 foreach my $v (keys %hcorrelgroup){ | |
| 226 my $count = 0; | |
| 227 if ($v ne $k){ | |
| 228 foreach my $w (keys %{$hcorrelgroup{$v}}){ | |
| 229 if($w eq $i){ | |
| 230 $count = 1; | |
| 231 push(@tdelete, $v); | |
| 232 } | |
| 233 } | |
| 234 } | |
| 235 if($count == 1){ | |
| 236 foreach my $w (keys %{$hcorrelgroup{$v}}){ | |
| 237 $hcorrelgroup{$k}{$w}=$hcorrelgroup{$v}{$w}; | |
| 238 } | |
| 239 delete($hcorrelgroup{$v}); | |
| 240 } | |
| 241 } | |
| 242 } | |
| 243 } | |
| 244 | |
| 245 foreach my $t (@tdelete){ | |
| 246 delete($hcorrelgroup{$t}); | |
| 247 } | |
| 248 | |
| 249 | |
| 250 ### Do it twice to see if it fix the problem of unmerge groups | |
| 251 | |
| 252 foreach my $k (keys %hcorrelgroup){ | |
| 253 foreach my $i (keys %{$hcorrelgroup{$k}}){ | |
| 254 foreach my $v (keys %hcorrelgroup){ | |
| 255 my $count = 0; | |
| 256 if ($v ne $k){ | |
| 257 foreach my $w (keys %{$hcorrelgroup{$v}}){ | |
| 258 if($w eq $i){ | |
| 259 $count = 1; | |
| 260 push(@tdelete, $v); | |
| 261 } | |
| 262 } | |
| 263 } | |
| 264 if($count == 1){ | |
| 265 foreach my $w (keys %{$hcorrelgroup{$v}}){ | |
| 266 $hcorrelgroup{$k}{$w}=$hcorrelgroup{$v}{$w}; | |
| 267 } | |
| 268 delete($hcorrelgroup{$v}); | |
| 269 } | |
| 270 } | |
| 271 } | |
| 272 } | |
| 273 | |
| 274 foreach my $t (@tdelete){ | |
| 275 delete($hcorrelgroup{$t}); | |
| 276 } | |
| 277 | |
| 278 print "Join groups that have been subdivided done\n"; | |
| 279 | |
| 280 ####################################################### | |
| 281 ### Addition of annotation information among groups ### | |
| 282 ####################################################### | |
| 283 | |
| 284 foreach my $k (keys %hcorrelgroup){ | |
| 285 foreach my $i (keys %{$hcorrelgroup{$k}}){ | |
| 286 foreach my $j (keys %{$hcorrelgroup{$k}}){ | |
| 287 my $count = 0; | |
| 288 if ($i ne $j){ | |
| 289 | |
| 290 my $a = $hrtmz{$i}{mz}; | |
| 291 my $b = $hrtmz{$j}{mz}; | |
| 292 | |
| 293 my $diff = $a - $b; | |
| 294 my $sign; | |
| 295 if($diff>0){ | |
| 296 $sign="+"; | |
| 297 } | |
| 298 if($diff<0){ | |
| 299 $sign="-"; | |
| 300 } | |
| 301 $diff = abs($diff); | |
| 302 | |
| 303 foreach my $z (keys %{$refhmass}){ | |
| 304 | |
| 305 foreach my $y (keys %{$refhmass->{$z}}){ | |
| 306 my $ym = $y - $mass_threshold; | |
| 307 my $yp = $y + $mass_threshold; | |
| 308 | |
| 309 | |
| 310 if(($diff <= $yp) && ($diff >= $ym)){ | |
| 311 my $diff_list = $diff - $y; | |
| 312 $diff_list = abs($diff_list); | |
| 313 $diff_list = sprintf ("%0.6f", $diff_list); | |
| 314 | |
| 315 if($hcorrelgroup{$k}{$i} eq 1){ | |
| 316 my $val = "@".$j."|".$sign."(".$z.")(".$diff_list.")|"; | |
| 317 $hcorrelgroup{$k}{$i}=$val; | |
| 318 $count ++; | |
| 319 } | |
| 320 else{ | |
| 321 if($count == 0){ | |
| 322 my $val = "@".$j."|".$sign."(".$z.")(".$diff_list.")|"; | |
| 323 $hcorrelgroup{$k}{$i}.=$val; | |
| 324 $count ++; | |
| 325 } | |
| 326 else{ | |
| 327 my $val = $sign."(".$z.")(".$diff_list.")|"; | |
| 328 $hcorrelgroup{$k}{$i}.=$val; | |
| 329 $count ++; | |
| 330 } | |
| 331 } | |
| 332 } | |
| 333 } | |
| 334 } | |
| 335 } | |
| 336 } | |
| 337 } | |
| 338 } | |
| 339 | |
| 340 | |
| 341 print "Addition of annotation information among groups done\n"; | |
| 342 | |
| 343 | |
| 344 #################################################### | |
| 345 ### Choose the representative ion for each group ### | |
| 346 #################################################### | |
| 347 | |
| 348 my %hgrouprepres; | |
| 349 | |
| 350 open(F3, $dataMatrix); | |
| 351 | |
| 352 while (my $line = <F3>){ | |
| 353 chomp $line; | |
| 354 | |
| 355 my @tline = split (/\t/, $line); | |
| 356 | |
| 357 foreach my $k (keys %hcorrelgroup){ | |
| 358 foreach my $i (keys %{$hcorrelgroup{$k}}){ | |
| 359 if($tline[0] eq $i){ | |
| 360 $hgrouprepres{$k}{$i}{mass}=$hrtmz{$tline[0]}{mz}; | |
| 361 my $intensity; | |
| 362 my $nbsubjects=0; | |
| 363 for(my $y=1;$y<scalar(@tline);$y++){ | |
| 364 $intensity += $tline[$y]; | |
| 365 $nbsubjects ++; | |
| 366 } | |
| 367 my $meanintensity = $intensity/$nbsubjects; | |
| 368 $hgrouprepres{$k}{$i}{intensity}=$meanintensity; | |
| 369 $hgrouprepres{$k}{$i}{squaredmassint}=($hgrouprepres{$k}{$i}{mass}**2)/($hgrouprepres{$k}{$i}{intensity}); | |
| 370 } | |
| 371 } | |
| 372 } | |
| 373 } | |
| 374 close F3; | |
| 375 | |
| 376 foreach my $z (keys %hgrouprepres){ | |
| 377 my $max_intensity = 0; | |
| 378 my $max_int_ion = ""; | |
| 379 my $max_mass = 0; | |
| 380 my $max_mass_ion = ""; | |
| 381 my $max_squared = 0; | |
| 382 my $max_squared_ion = ""; | |
| 383 foreach my $w (keys %{$hgrouprepres{$z}}){ | |
| 384 if($hgrouprepres{$z}{$w}{intensity} > $max_intensity){ | |
| 385 $max_intensity = $hgrouprepres{$z}{$w}{intensity}; | |
| 386 $max_int_ion = $w; | |
| 387 } | |
| 388 if($hgrouprepres{$z}{$w}{mass} > $max_mass){ | |
| 389 $max_mass = $hgrouprepres{$z}{$w}{mass}; | |
| 390 $max_mass_ion = $w; | |
| 391 } | |
| 392 if($hgrouprepres{$z}{$w}{squaredmassint} > $max_squared){ | |
| 393 $max_squared = $hgrouprepres{$z}{$w}{squaredmassint}; | |
| 394 $max_squared_ion = $w; | |
| 395 } | |
| 396 } | |
| 397 | |
| 398 my $max_int_max_mass_ion=""; | |
| 399 | |
| 400 if($repres_opt eq "max_intensity_max_mass"){ | |
| 401 my %hfirst; | |
| 402 my $first=0; | |
| 403 foreach my $w (reverse sort {$hgrouprepres{$z}{$a}{intensity} <=> $hgrouprepres{$z}{$b}{intensity} } keys %{$hgrouprepres{$z}}){ | |
| 404 $first ++; | |
| 405 if ($first <= 3){ | |
| 406 $hfirst{$w} = $hgrouprepres{$z}{$w}{intensity}; | |
| 407 } | |
| 408 } | |
| 409 | |
| 410 my $first_2 = 0; | |
| 411 my $intens_max = 0; | |
| 412 my $mass_max = 0; | |
| 413 | |
| 414 foreach my $y (reverse sort {$hfirst{$a} <=> $hfirst{$b}} keys %hfirst){ | |
| 415 | |
| 416 $first_2 ++; | |
| 417 if($first_2 == 1){ | |
| 418 $intens_max = $hfirst{$y}; | |
| 419 if($intensity_threshold > $intens_max){ | |
| 420 $intensity_threshold = 0; | |
| 421 } | |
| 422 $max_int_max_mass_ion = $y; | |
| 423 $mass_max = $hgrouprepres{$z}{$y}{mass}; | |
| 424 } | |
| 425 if($hgrouprepres{$z}{$y}{mass} > $mass_max){ | |
| 426 if($hfirst{$y}>$intensity_threshold){ | |
| 427 my $a = $intens_max * $intensity_pourc; | |
| 428 if($hfirst{$y} > $a){ | |
| 429 $max_int_max_mass_ion = $y; | |
| 430 $mass_max = $hgrouprepres{$z}{$y}{mass}; | |
| 431 } | |
| 432 } | |
| 433 } | |
| 434 } | |
| 435 } | |
| 436 | |
| 437 $hgrouprepres{$z}{max_int}=$max_int_ion; | |
| 438 $hgrouprepres{$z}{max_mass}=$max_mass_ion; | |
| 439 $hgrouprepres{$z}{max_squared}=$max_squared_ion; | |
| 440 $hgrouprepres{$z}{max_int_max_mass}=$max_int_max_mass_ion; | |
| 441 | |
| 442 } | |
| 443 | |
| 444 | |
| 445 print "Choose the representative ion for each group done\n"; | |
| 446 | |
| 447 ############################################################################# | |
| 448 ### Addition of annotation information relative to the representative ion ### | |
| 449 ############################################################################# | |
| 450 | |
| 451 my %hreprescomparison; | |
| 452 | |
| 453 my $representative=""; | |
| 454 | |
| 455 if($opt != 1){ | |
| 456 foreach my $k (keys %hcorrelgroup){ | |
| 457 foreach my $i (keys %{$hcorrelgroup{$k}}){ | |
| 458 | |
| 459 if($repres_opt eq "mass"){$representative = $hgrouprepres{$k}{max_mass}} | |
| 460 if($repres_opt eq "intensity"){$representative = $hgrouprepres{$k}{max_int}} | |
| 461 if($repres_opt eq "mixt"){$representative = $hgrouprepres{$k}{max_squared}} | |
| 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}{$tline[0]}\t"; | |
| 569 | |
| 570 } | |
| 571 else{ | |
| 572 print F4 "\t"; | |
| 573 } | |
| 574 } | |
| 575 | |
| 576 if($repres_opt eq "intensity"){ | |
| 577 if($tline[0] eq $hgrouprepres{$v}{max_int}){ | |
| 578 print F4 "1\t"; | |
| 579 } | |
| 580 else{ | |
| 581 print F4 "0\t"; | |
| 582 } | |
| 583 $find = 1; | |
| 584 } | |
| 585 if($repres_opt eq "mass"){ | |
| 586 if($tline[0] eq $hgrouprepres{$v}{max_mass}){ | |
| 587 print F4 "1\t"; | |
| 588 } | |
| 589 else{ | |
| 590 print F4 "0\t"; | |
| 591 } | |
| 592 $find = 1; | |
| 593 } | |
| 594 if($repres_opt eq "mixt"){ | |
| 595 if($tline[0] eq $hgrouprepres{$v}{max_squared}){ | |
| 596 print F4 "1\t"; | |
| 597 } | |
| 598 else{ | |
| 599 print F4 "0\t"; | |
| 600 } | |
| 601 $find = 1; | |
| 602 } | |
| 603 if($repres_opt eq "max_intensity_max_mass"){ | |
| 604 if($tline[0] eq $hgrouprepres{$v}{max_int_max_mass}){ | |
| 605 print F4 "1\t"; | |
| 606 } | |
| 607 else{ | |
| 608 print F4 "0\t"; | |
| 609 } | |
| 610 $find = 1; | |
| 611 } | |
| 612 | |
| 613 if($repres_opt eq "intensity"){print F4 "$hgrouprepres{$v}{max_int}\t"} | |
| 614 if($repres_opt eq "mass"){print F4 "$hgrouprepres{$v}{max_mass}\t"} | |
| 615 if($repres_opt eq "mixt"){print F4 "$hgrouprepres{$v}{max_squared}\t"} | |
| 616 if($repres_opt eq "max_intensity_max_mass"){print F4 "$hgrouprepres{$v}{max_int_max_mass}\t"} | |
| 617 | |
| 618 if(defined($hreprescomparison{$v}{$tline[0]}{repres_diff})){ | |
| 619 print F4 "$hreprescomparison{$v}{$tline[0]}{repres_diff}\n"; | |
| 620 } | |
| 621 else{ | |
| 622 print F4 "-\n"; | |
| 623 } | |
| 624 } | |
| 625 } | |
| 626 if($find == 0){ | |
| 627 $groupct ++; | |
| 628 my $group = "group".$groupct; | |
| 629 if($opt != 1){ | |
| 630 print F4 "$line\t$group\t-\t-\t-\t-\n"; | |
| 631 } | |
| 632 else{ | |
| 633 print F4 "$line\t$group\t-\t-\n"; | |
| 634 } | |
| 635 } | |
| 636 } | |
| 637 $line_nb ++; | |
| 638 } | |
| 639 | |
| 640 print "Print in result file done\n"; | |
| 641 | |
| 642 print "All steps done\n"; | |
| 643 |