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comparison SNiPloid.pl @ 0:58111b3965b2 draft default tip

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author dereeper
date Thu, 01 Nov 2012 09:35:05 -0400
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1 #!/usr/bin/perl
2
3 use Getopt::Long;
4 use Switch;
5 use Tie::File;
6
7 #####################################################
8 # #
9 # @@@@ @ @ @ @@@@ @ @ @ #
10 # @ @@ @ @ @ @ @ #
11 # @@@ @ @ @ @ @@@@ @ @@@ @ @@@@ #
12 # @ @ @@ @ @ @ @ @ @ @ @ #
13 # @@@@ @ @ @ @ @ @@@ @ @@@ #
14 # #
15 #####################################################
16
17 ###############################################################################################################
18 #
19 # SNiPloid
20 # Author : Marine PERALTA
21 #
22 ###############################################################################################################
23 #
24 # Galaxy Version
25 #
26 ###############################################################################################################
27
28 #___________________________________
29 # Samples names
30 #-----------------------------------
31 $polyploidName = "" ;
32 $polyploid2Name = "" ; #
33 $genome1Name = "" ;
34 $genome2Name = "" ;
35 #___________________________________
36 # VCF files
37 #-----------------------------------
38 $VCFpolyploid = "" ;
39 $VCFpolyploid2 = "" ; #
40 $VCFgenome1 = "" ;
41 $VCFgenome2 = "" ;
42 $merged_VCF = "" ; # Polyploid + Genome1 + Genome 2
43 #___________________________________
44 # Depth of Coverage File
45 #-----------------------------------
46 $DOCpolyploid = "" ;
47 $DOCpolyploid2 = "" ; #
48 $DOCgenome1 = "" ;
49 $DOCgenome2 = "" ;
50 $merged_DOC = "" ; # Polyploid + Genome1 + Genome 2
51 #___________________________________
52 # Depth for each sample
53 #-----------------------------------
54 $depthPolyploid = 0 ;
55 $depthPolyploid2 = 0 ; #
56 $depthGenome1 = 0 ;
57 $depthGenome2 = 0 ;
58 #___________________________________
59 # Output Files
60 #-----------------------------------
61 $SNP_csv = "SNP_tab.txt";
62 $SNP_html = "SNP_view.html";
63 $SNP_count = "SNP_synthesis_tab.html";
64 $SNP_count_csv = "SNP_synthesis_tab.txt";
65 #___________________________________
66 # Other parameters
67 #-----------------------------------
68 $enableLowQuality = 0 ; #default value for enable quality SNP = only PASS SNP are considered
69 $ref = 0 ; # default parameter = extern
70
71 $filtre_ouPas = 0 ;
72 $value_filter_p1 = 0 ;
73 $value_filter_p2 = 0 ;
74
75 $REPimages = "img_sniploid/";
76
77 $poly_poly_analysis = 0 ;
78
79
80 my $usage = qq~
81 Basic usage
82
83 For comparison between a polyploid and its parental diploid genomes:
84
85 $0 --vp <VCF_polyploid> --vg1 <VCF_diploid> --cpp <depth_polyploid> --cg1 <depth_diploid> --dp <min_depth_polyploid> --dg1 <min_depth_diploid> --ref 1
86
87 For comparison between 2 polyploids:
88
89 $0 --vp <VCF_polyploid1> --vp2 <VCF_polyploid2> --cpp <depth_polyploid1> --cpp2 <depth_polyploid2> --dp <min_depth_polyploid1> --dp2 <min_depth_polyploid2>
90
91 Usage:$0 <args>
92 where <args> are:
93
94 --vp <VCF file for polyploid>
95 --vp2 <VCF file for polyploid 2>
96 --vg1 <VCF file for diploid genome 1>
97 --vg2 <VCF file for diploid genome 2>
98
99 --cpp <Depth file for polyploid>
100 --cpp2 <Depth file for polyploid 2>
101 --cg1 <Depth file for diploid genome 1>
102 --cg2 <Depth file for diploid genome 2>
103
104 --dp <Minimum read depth at a position to make a call for polyploid>
105 --dp2 <Minimum read depth at a position to make a call for polyploid 2>
106 --dg1 <Minimum read depth at a position to make a call for diploid genome 1>
107 --dg2 <Minimum read depth at a position to make a call for diploid genome 2>
108
109 --oc <Output file name for SNP list in csv>
110 --oh <Output file name for SNP list in HTML>
111 --ocs <Output file name for SNP count per gene in csv>
112 --ohs <Output file name for SNP count per gene in HTML>
113
114 --vfp1 <Minimul allele frequency to consider as variant for polyploid 1 (in %). Default: 0>
115 --vfp2 <Minimul allele frequency to consider as variant for polyploid 2 (in %). Default: 0>
116
117 --elq <Enable low quality SNP tag. Default: 0>
118 --gn2 <Specify a name for diploid genome 2>
119 --ref <The reference must be included in the analysis as diploid genome. Default: 0>
120 ~;
121 $usage .= "\n";
122
123
124 =pod
125 Add option for "Heterozygosity"
126 Enable "heterozygosity" for genome 1 (reference intern) - not necessary...
127 Enable "heterozygosity" for genome 1 and genome 2 (reference extern)
128 =cut
129
130 GetOptions (
131 # "pn=s" => \$polyploidName,
132 # "pn2=s" => \$polyploid2Name, #
133 # "gn1=s" => \$genome1Name,
134 "gn2=s" => \$genome2Name,
135 "vp=s" => \$VCFpolyploid,
136 "vp2=s" => \$VCFpolyploid2, #
137 "vg1=s" => \$VCFgenome1,
138 "vg2=s" => \$VCFgenome2,
139 "vm=s" => \$merged_VCF,
140 "cpp=s" => \$DOCpolyploid,
141 "cpp2=s" => \$DOCpolyploid2, #
142 "cg1=s" => \$DOCgenome1,
143 "cg2=s" => \$DOCgenome2,
144 "cm=s" => \$merged_DOC,
145 "dp=i" => \$depthPolyploid,
146 "dp2=i" => \$depthPolyploid2, #
147 "dg1=i" => \$depthGenome1,
148 "dg2=i" => \$depthGenome2,
149 "oc=s" => \$SNP_csv,
150 "oh=s" => \$SNP_html,
151 "ohs=s" => \$SNP_count,
152 "ocs=s" => \$SNP_count_csv,
153 "elq=i" => \$enableLowQuality,
154 "ref=i" => \$ref,
155 #"fop=i" => \$filtre_ouPas,
156 "vfp1=i" => \$value_filter_p1,
157 "vfp2=i" => \$value_filter_p2,
158 "img=s" => \$REPimages
159 # h = i = > \ $heterozygosity ,
160 );
161
162
163 # Validation - Samples names
164
165
166 die $usage
167 if ( (!$VCFgenome1 || !$DOCgenome1 ) && (!$VCFpolyploid || !$DOCpolyploid) || (!$VCFpolyploid2 || !$DOCpolyploid2 ) && (!$VCFpolyploid || !$DOCpolyploid));
168
169
170
171 %intervalle1 ;
172 %intervalle2 ;
173 %snp = () ;
174 my %snp_final ;
175 my %five = () ;
176 my %phased_regions = () ;
177
178 $nbTotGenes = 0 ;
179 $nbTotGenesVal = 0 ;
180 $nbTotGenesAna = 0 ;
181
182
183 if ($VCFpolyploid2 ne "") {
184 $poly_poly_analysis = 1 ;
185 }
186
187 # if ($polyploidName eq "") {
188 # print STDOUT "*** /!\\ ERROR: Missing name for polyploid - You have to specify a name for the polyploid species [--pn \"polyploid_name\"] $!" ;
189 # die ("*** /!\\ ERROR: Missing name for polyploid - You have to specify a name for the polyploid species [--pn \"polyploid_name\"] $!") ;
190 # }
191
192 if ($poly_poly_analysis == 1) {
193 print STDOUT "\nAnalysis Type: Polyploid vs Polyploid\n---------------------------------------";
194 # print STDOUT "\nPolyploid 1: ".$polyploidName ;
195 # print STDOUT "\nPolyploid 2:".$polyploid2Name ;
196 # if ($polyploid2Name eq "") {
197 # print STDOUT "*** /!\\ ERROR: Missing name for polyploid 2 - You have to specify a name for the polyploid species 2 [--pn2 \"polyploid_2_name\"] $!" ;
198 # die ("*** /!\\ ERROR: Missing name for polyploid - You have to specify a name for the polyploid species 2 [--pn \"polyploid_2_name\"] $!") ;
199 # }
200 }
201 else {
202 print STDOUT "\nAnalysis Type: Polyploid vs Parental Genomes\n---------------------------------------";
203 # print STDOUT "\nPolyploid: ".$polyploidName ;
204 # print STDOUT "\nGenome 1: ".$genome1Name ;
205 # print STDOUT "\nGenome 2: ".$genome2Name ;
206 # if ($genome1Name eq "") {
207 # die ("*** /!\\ ERROR: Missing name for genome 1 - You have to specify a name for the genome 1 species") ;
208 # }
209 # if ($genome2Name eq "") {
210 # die ("*** /!\\ ERROR: Missing name for genome 2 - You have to specify a name for the genome 2 species") ;
211 # }
212 # Validation - depth
213 if ($depthPolyploid == 0) {
214 die ("*** /!\\ ERROR: Missing depth information for polyploid");
215 }
216 if ($depthGenome1 == 0) {
217 die ("*** /!\\ ERROR: Missing depth information for genome 1");
218 }
219 if ($ref == 0 && $depthGenome2 == 0) {
220 die ("*** /!\\ ERROR: Missing depth information for genome 2");
221 }
222 }
223
224
225
226
227 $time = time ;
228
229
230 ################################################################
231 # 1) Polyploid vs Polyploid analysis
232 ################################################################
233 if ($poly_poly_analysis == 1) {
234 #print STDOUT "\n PASS";
235 &Intervall_part1($DOCpolyploid) ;
236 &Intervall_part2($DOCpolyploid2,$depthPolyploid2) ;
237
238 &VCF_Analysis($VCFpolyploid);
239 &VCF_Analysis($VCFpolyploid2);
240 # CSS, titles, img, etc.
241 &intro_output ;
242 &poly_poly_output ;
243 }
244 ################################################################
245 # 2) Polyploid vs Parental Diploid Genomes Analysis
246 ################################################################
247 else {
248
249 # PART 1 : CREATING COMMON INTERVALS
250
251 &Intervall_part1($DOCpolyploid) ;
252 &Intervall_part2($DOCgenome1,$depthGenome1) ;
253 if ($ref == 0) { # genome2 => no parental genome as reference
254 &Intervall_part2($DOCgenome2,$depthGenome2) ;
255 }
256
257 # PART 2 and 3 : CREATING SNP TAB AND OUTPUTS
258
259 # VCF_Analysis : Create SNP hash and phasing
260
261 &VCF_Analysis($VCFpolyploid);
262 if ($ref == 1) { # Reference = one of two parental genomes
263 &VCF_Analysis($VCFgenome1);
264 # CSS, titles, img, etc.
265 &intro_output ;
266 # SNP Comparison and display
267 &int_output ;
268 }
269 else { # Extern Reference
270 &VCF_Analysis($VCFgenome1);
271 &VCF_Analysis($VCFgenome2);
272 # CSS, titles, img, etc.
273 &intro_output ;
274 # SNP Comparison and display
275 &ext_output ;
276 }
277 }
278
279
280
281
282 sub Intervall_part1 {
283 my(@args) = @_;
284 #print STDOUT "\nTEST ::: ".$args[0] ;
285 open (TABSNP, $args[0]) or die ("Pbm a l'ouverture du fichier : $args[0]");
286 @DOC = <TABSNP> ;
287 close TABSNP ;
288
289 $rec = 0 ;
290 $position_pre ;
291 $val_deb = "";
292 $val_fin = "";
293 $name_pre = "";
294
295
296 foreach $line(@DOC) {
297 if ($line ne $DOC[0]) {
298 @ligne = split(/\t/ , $line);
299 @position = split(/:/ , $ligne[0]);
300 $name_gene = $position[0] ;
301
302 if ($merged == 0) { # 1st File - Polyploid
303 $depthcov = $ligne[1] ;
304 if ($name_gene){
305 if ($depthcov >= $depthPolyploid){
306 if ($rec == 0) {
307 $position_deb = $position[1] ;
308 $val_deb = $position_deb."-"; # Intervalle start position
309 }
310 $rec = 1 ;
311 }
312 if ($depthcov < $depthPolyploid){
313 if ($rec == 1) {
314 $position_fin = $position_pre ;
315 $val_fin = $val_deb.$position_fin ; # Intervalle end position
316 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
317 }
318 $rec = 0 ;
319 }
320 }
321 }
322 else { # Merged files (2 or 3 species)
323 if ($ref == 0) { # 3 species
324 $depthcov1 = $ligne[$indiceGenome2] ;
325 $depthcov2 = $ligne[$indicePolyploid1] ;
326 $depthcov3 = $ligne[$indiceGenome1] ;
327 if ($name_gene){
328 if (($depthcov1 >= $depthGenome2) && ($depthcov2 >= $depthPolyploid)&& ($depthcov3 >= $depthGenome1)){
329 if ($rec == 0) {
330 $position_deb = $position[1] ;
331 $val_deb = $position_deb."-";
332 }
333 $rec = 1 ;
334 }
335 if (($depthcov1 < $depthGenome2) || ($depthcov2 < $depthPolyploid) || ($depthcov3 < $depthGenome1)){
336 if ($rec == 1) {
337 $position_fin = $position_pre ;
338 $val_fin = $val_deb.$position_fin ;
339 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
340 }
341 $rec = 0 ;
342 }
343 }
344 }
345 else { # 2 species
346 $depthcov1 = $ligne[$indicePolyploid1] ;
347 $depthcov2 = $ligne[$indiceGenome1] ;
348 if ($name_gene){
349 if (($depthcov1 >= $depthPolyploid) && ($depthcov2 >= $depthGenome1)){
350 if ($rec == 0) {
351 $position_deb = $position[1] ;
352 $val_deb = $position_deb."-";
353 }
354 $rec = 1 ;
355 }
356 if (($depthcov1 < $depthPolyploid) || ($depthcov2 < $depthGenome1)){
357 if ($rec == 1) {
358 $position_fin = $position_pre ;
359 $val_fin = $val_deb.$position_fin ;
360 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
361 }
362 $rec = 0 ;
363 }
364 }
365 }
366 }
367 $position_pre = $position[1] ;
368 $gene_pre = $name_gene ;
369 }
370 }
371
372 return (%intervalle1) ;
373
374 }
375 sub Intervall_part2 {
376
377 my(@args) = @_;
378 #print "\nintervall part 2 : $args[1]";
379
380 open (TABSNP, $args[0]) or die ("Pbm a l'ouverture du fichier : $args[0]");
381 #print STDOUT "\n$args[0]";
382 @DOC = <TABSNP> ;
383 my %tab ;
384 foreach $li(@DOC) {
385 if ($li =~ /^(.+):(.+)\t(.+)\t.+\t.+$/) {
386 $tab{$1}{$2} = $3;
387 }
388 }
389 close TABSNP ;
390
391
392
393 $rec = 0 ;
394 $position_pre ;
395 $val_deb = "";
396 $val_fin = "";
397
398 foreach my $interval(sort (keys(%intervalle1))){
399
400 my $ref = $intervalle1{$interval};
401 my %intervalls = %$ref;
402 $name_gene = $interval ;
403
404 foreach my $intervall(sort (keys(%intervalls))){
405 $final = 2 ;
406 $rec = 0 ;
407 ($debut,$fin) = split(/-/,$intervall);
408 for ($i=$debut; $i <=$fin; $i++) {
409 if ($tab{$interval}{$i} >= $args[1]){
410 if ($rec == 0) {
411 $position_deb = $i ;
412 $val_deb = $position_deb."-";
413 }
414 $rec = 1 ;
415 $final = 0 ;
416 }
417 if ($tab{$interval}{$i} < $args[1]){
418 $final = 1 ;
419 if ($rec == 1) {
420 $position_fin = $i-1 ;
421 $val_fin = $val_deb.$position_fin ;
422 $intervalle2{$name_gene}{$val_fin} = "ok" ;
423 }
424 $rec = 0 ;
425 }
426 }
427 if ($final == 0) {
428 $val_fin = $val_deb.$fin ;
429 $intervalle2{$name_gene}{$val_fin} = "ok" ;
430 }
431 }
432 }
433 if ($VCFgenome2 ne ""){
434 %intervalle1 = %intervalle2 ;
435 }
436
437 foreach my $interval(sort (keys(%intervalle2))){
438 my $ref = $intervalle2{$interval};
439 my %intervalls = %$ref;
440 $name_gene = $interval ;
441 }
442
443 return (%intervalle2) ;
444 }
445
446 sub VCF_Analysis {
447 %snp_final = () ;
448 $compt_phasing = 0 ;
449 $compt_five = 0 ;
450 my(@args) = @_;
451
452 open (TABSNP, "$args[0]") or die ("ERROR : file $args[0] don't exists");
453 @VCF = <TABSNP> ;
454 close TABSNP ;
455
456 ###########################################
457 # test if VCF was filtered
458 ###########################################
459 my $vcf_file = $args[0];
460 my $is_filtered = `grep PASS $vcf_file`;
461 my $pass = ".";
462 if ($is_filtered)
463 {
464 $pass = "PASS";
465 }
466
467 print "$pass\n";
468
469 foreach $line(@VCF){
470 if ($line =~ /^#CHROM.+FORMAT\t(.+)$/) {
471 $name_record = $1 ;
472 }
473 if ($line !~ /^#/){
474 @infos_line = split(/\t/,$line) ;
475 $gene = $infos_line[0];
476 $position = $infos_line[1];
477 $ref_allele = $infos_line[3];
478 $alt_allele = $infos_line[4];
479 $snp_code = "[$ref_allele/$alt_allele]";
480 $quality_of_snp = $infos_line[6];
481 $depth_recuperation = $infos_line[7];
482 $alleles = $infos_line[9];
483
484 ($GT,$AD,$FDP,$GQ,$PL) = split(":",$alleles);
485
486
487 # PHASING
488
489 if (($GT =~ /\|/) && ($previous_GT =~ /\//)) { # initialisation région
490 $compt_phasing ++ ;
491 $phased_regions{$gene}{$compt_phasing}{$previous_position} = $previous_GT ;
492 $phased_regions{$gene}{$compt_phasing}{$position} = $GT ;
493 }
494 if (($GT =~ /\|/) && ($previous_GT =~ /\|/)) { # extension région
495 $phased_regions{$gene}{$compt_phasing}{$position} = $GT ;
496 }
497
498
499 # $FDP = Filtered Depth
500 # $DP = Total Depth
501
502 ($AC,$AF,$AN,$DP,$DS,$Dels,$HRun,$HaplotypeScore,$MQ,$MQ0,$QD,$SB,$sumGLbyD) = split(";",$depth_recuperation);
503
504 ($sub1,$sub2) = split(",",$AD);
505 $somme = $sub1 + $sub2 ;
506
507 if ($somme == 0 ) {
508 print STDOUT "ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"";
509 die ("ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"");
510 }
511 else {
512 $ratio = ($sub1/($sub1+$sub2))*100;
513 $ratio = sprintf("%.0f", $ratio);
514 }
515
516 @DP = split ("=",$DP) ;
517
518 $test_inside_interval = 0 ;
519
520 my $ref = $intervalle2{$gene};
521 my %hash = %$ref;
522
523 foreach my $interval(keys(%hash)){
524 my @pos = split(/-/,$interval) ;
525 if ($position >= $pos[0] && $position <= $pos[1]) {
526 $test_inside_interval = 1 ;
527 last ;
528 }
529 }
530
531 # ENABLE LOW_QUALITY SNP
532 if ($enableLowQuality == 1) {
533
534 if ($test_inside_interval == 1 ){ #
535 if ($args[0] eq $VCFpolyploid) { # Polyploid
536 $polyploidName = $name_record ;
537 $snp{$gene}{$position} = $snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
538 }
539 else {
540 if ($args[0] eq $VCFgenome1) { # genome1
541 $genome1Name = $name_record ;
542 if (exists $snp{$gene}{$position}) { # if polyploid SNP
543 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT ;
544
545 ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp{$gene}{$position});
546 @recupAlleles = split(/\[/,$code_snp);
547 @recupAlleles = split(/\]/,$recupAlleles[1]);
548 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
549 @recupAlleles = split(/\[/,$code_G1);
550 @recupAlleles = split(/\]/,$recupAlleles[1]);
551 ($alRef,$code_G1) = split(/\//,$recupAlleles[0]);
552
553 #print "\nINFOS\n".$GT_poly."\t";
554 #print $GT_G1."\t";
555 #print $code_G1."\t";
556 #print $alAltP."\n";
557 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) {
558 $five{$gene}{$position} = $GT_poly ;
559 }
560 }
561 else { # if no polyploid SNP, key is empty
562 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$GT ;
563 }
564 }
565 else { # genome2
566 if ($args[0] eq $VCFgenome2) {
567 $genome2Name = $name_record ;
568 if (exists $snp{$gene}{$position}) { # if polyploid SNP
569 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT;
570 }
571 else { # if no polyploid SNP and no genome1, key is empty
572 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$ref_allele."\t\t".$snp_code."\t".$GT ;
573 }
574 }
575 }
576 if ($args[0] eq $VCFpolyploid2) { # polyploid2
577 $polyploid2Name = $name_record ;
578 if (exists $snp{$gene}{$position}) { # if polyploid SNP
579 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
580 }
581 else { # if no polyploid SNP, key is empty
582 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
583 }
584 }
585 }
586 }
587 }
588 # ONLY PASS SNP CONSIDERED
589 else {
590 if (($test_inside_interval == 1 ) && ($quality_of_snp eq $pass) && ($snp{$gene}{$position} ne "LQ")){ #
591 if ($args[0] eq $VCFpolyploid) { # Polyploid
592 $polyploidName = $name_record ;
593 $snp{$gene}{$position} = $snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
594 }
595 else {
596 if ($args[0] eq $VCFgenome1) { # genome1
597 $genome1Name = $name_record ;
598 if (exists $snp{$gene}{$position}) { # if polyploid SNP
599 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT ;
600
601 ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp{$gene}{$position});
602 @recupAlleles = split(/\[/,$code_snp);
603 @recupAlleles = split(/\]/,$recupAlleles[1]);
604 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
605 @recupAlleles = split(/\[/,$code_G1);
606 @recupAlleles = split(/\]/,$recupAlleles[1]);
607 ($alRef,$code_G1) = split(/\//,$recupAlleles[0]);
608
609 #print "\nINFOS\n".$GT_poly."\t";
610 #print $GT_G1."\t";
611 #print $code_G1."\t";
612 #print $alAltP."\n";
613 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) {
614 $five{$gene}{$position} = $GT_poly ;
615 }
616 }
617 else { # if no polyploid SNP, key is empty
618 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$GT ;
619 }
620 }
621 else { # genome2
622 if ($args[0] eq $VCFgenome2) {
623 $genome2Name = $name_record ;
624 if (exists $snp{$gene}{$position}) { # if polyploid SNP
625 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT;
626 }
627 else { # if no polyploid SNP and no genome1, key is empty
628 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$ref_allele."\t\t".$snp_code."\t".$GT ;
629 }
630 }
631 }
632 if ($args[0] eq $VCFpolyploid2) { # polyploid2
633 $polyploid2Name = $name_record ;
634 if (exists $snp{$gene}{$position}) { # if polyploid SNP
635 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
636 }
637 else { # if no polyploid SNP, key is empty
638 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
639 }
640 }
641 }
642 }
643 else {
644 if ($quality_of_snp ne $pass) {
645 $snp{$gene}{$position} = "LQ";
646 }
647 }
648 }
649 ################################################################################################################################
650 }
651 $previous_GT = $GT ;
652 $previous_position = $position ;
653 }
654 foreach my $s(sort(keys(%snp))){
655 my $ref = $snp{$s};
656 my %hash = %$ref;
657 foreach my $snip(keys(%hash)){
658 if ($snp{$s}{$snip} ne "LQ"){
659 $snp_final{$s}{$snip} = $snp{$s}{$snip} ;
660 }
661 }
662 }
663 return (%snp_final) ;
664 }
665
666 sub intro_output {
667
668 ###########################################################
669 # ANALYSE - CREATION FICHIERS DE SORTIE #
670 ###########################################################
671
672 # Ouverture des fichiers
673 open (HTMLSNP, ">$SNP_html");
674 open (TABSNP, ">$SNP_csv");
675 open (HTMLCOUNT, ">$SNP_count");
676 open (TABCOUNT, ">$SNP_count_csv");
677
678 print HMTL "<html>\n";
679 print HTMLCOUNT "<html>\n";
680
681 print HTMLSNP "<head>\n";
682 print HTMLCOUNT "<head>\n";
683
684 #####################################################
685 # CSS #
686 #####################################################
687 print HTMLSNP "<style type=\"text/css\">\n";
688
689 print HTMLSNP "th {\n";
690 print HTMLSNP " border-color:black;\n";
691 print HTMLSNP " border-style:solid; \n";
692 print HTMLSNP " border-width:3px;\n";
693 print HTMLSNP " font-family: calibri;\n";
694 print HTMLSNP " }\n";
695
696 print HTMLSNP "body {text-align:center;}\n";
697
698 print HTMLSNP "table {\n";
699 print HTMLSNP " border-color:black;\n";
700 print HTMLSNP " margin:auto;\n";
701 print HTMLSNP " border-collapse: collapse;\n";
702 print HTMLSNP " border-width:3px; \n";
703 print HTMLSNP " border-style:solid; \n";
704 print HTMLSNP " }\n";
705
706 print HTMLSNP ".bord1 { \n";
707
708 print HTMLSNP " font-size: 11pt;\n";
709 print HTMLSNP " font-family: calibri;\n";
710 print HTMLSNP " border-width:1px;\n";
711 print HTMLSNP " border-top:3px;\n";
712 print HTMLSNP " border-left:3px;\n";
713 print HTMLSNP " border-right:3px;\n";
714 print HTMLSNP " border-style:solid; \n";
715 print HTMLSNP " border-color:black;\n";
716 print HTMLSNP " background-color : #c6c3bd; \n";
717 print HTMLSNP " }\n";
718
719 print HTMLSNP ".bord2 { \n";
720
721 print HTMLSNP " font-size: 11pt;\n";
722 print HTMLSNP " font-family: calibri;\n";
723 print HTMLSNP " border-width:1px;\n";
724 print HTMLSNP " border-top:3px;\n";
725 print HTMLSNP " border-left:3px;\n";
726 print HTMLSNP " border-right:3px;\n";
727 print HTMLSNP " border-style:solid; \n";
728 print HTMLSNP " border-color:black;\n";
729 print HTMLSNP " background-color : #c6c3ee; \n";
730 print HTMLSNP " }\n";
731
732
733 print HTMLSNP "td { \n";
734 print HTMLSNP " border-color:black;\n";
735 print HTMLSNP " }\n";
736
737 print HTMLSNP ".tdm { \n";
738 print HTMLSNP " border-color:black;\n";
739 print HTMLSNP " border-left:3px;\n";
740 print HTMLSNP " }\n";
741
742
743 print HTMLSNP ".td1 { \n";
744 print HTMLSNP " border-color:black;\n";
745 print HTMLSNP " font-size: 11pt;\n";
746 print HTMLSNP " font-family: calibri;\n";
747 print HTMLSNP " border-width:1px;\n";
748 print HTMLSNP " border-left:3px;\n";
749 print HTMLSNP " border-right:3px;\n";
750 print HTMLSNP " border-style:solid; \n";
751 print HTMLSNP " background-color : #c6c3bd; \n";
752 print HTMLSNP " }\n";
753
754 print HTMLSNP ".td2 { \n";
755 print HTMLSNP " border-color:black;\n";
756 print HTMLSNP " font-size: 11pt;\n";
757 print HTMLSNP " font-family: calibri;\n";
758 print HTMLSNP " border-width:1px;\n";
759 print HTMLSNP " border-left:3px;\n";
760 print HTMLSNP " border-right:3px;\n";
761 print HTMLSNP " border-style:solid; \n";
762 print HTMLSNP " background-color : #c6c3ee; \n";
763 print HTMLSNP " }\n";
764
765 print HTMLSNP ".ted { \n";
766 print HTMLSNP " border-color:black;\n";
767 print HTMLSNP " font-weight : bold;\n";
768 print HTMLSNP " background-color : #A19EED; \n";
769 print HTMLSNP " }\n";
770
771 print HTMLSNP ".ted2 { \n";
772 print HTMLSNP " border-color:black;\n";
773 print HTMLSNP " font-weight : bold;\n";
774 print HTMLSNP " background-color : #9A9D7C; \n";
775 print HTMLSNP " }\n";
776
777 print HTMLSNP ".tedG { \n";
778 print HTMLSNP " border-left:3px;\n";
779 print HTMLSNP " border-style:solid; \n";
780 print HTMLSNP " border-color:black;\n";
781 print HTMLSNP " font-weight : bold;\n";
782 print HTMLSNP " background-color : #A19EED; \n";
783 print HTMLSNP " }\n";
784
785 print HTMLSNP ".tedG2 { \n";
786 print HTMLSNP " border-left:3px;\n";
787 print HTMLSNP " border-style:solid; \n";
788 print HTMLSNP " border-color:black;\n";
789 print HTMLSNP " font-weight : bold;\n";
790 print HTMLSNP " background-color : #9A9D7C; \n";
791 print HTMLSNP " }\n";
792
793 print HTMLSNP ".final { \n";
794 print HTMLSNP " border-left:3px;\n";
795 print HTMLSNP " border-right:0px;\n";
796 print HTMLSNP " border-top:0px;\n";
797 print HTMLSNP " border-bottom:0px;\n";
798 print HTMLSNP " border-style:solid; \n";
799 print HTMLSNP " border-color:black;\n";
800 print HTMLSNP " background-color : white; \n";
801 print HTMLSNP " }\n";
802
803 print HTMLSNP ".auto-style1 {";
804 print HTMLSNP " font-weight: normal;";
805 print HTMLSNP " font-size: x-small;";
806 print HTMLSNP "}";
807
808
809 print HTMLSNP "</style>\n";
810
811 print HTMLCOUNT "<style type=\"text/css\">\n";
812
813 print HTMLCOUNT "th {\n";
814 print HTMLCOUNT " border-style:solid; \n";
815 print HTMLCOUNT " border-color:black;\n";
816 print HTMLCOUNT " border-width:3px;\n";
817 print HTMLCOUNT " font-family:calibri;\n";
818 print HTMLCOUNT " }\n";
819
820 print HTMLCOUNT "table {\n";
821 print HTMLCOUNT " margin:auto;\n";
822 print HTMLCOUNT " border-collapse: collapse;\n";
823 print HTMLCOUNT " border-width:3px; \n";
824 print HTMLCOUNT " border-style:solid; \n";
825 print HTMLCOUNT " border-color:black;\n";
826 print HTMLCOUNT " }\n";
827
828 print HTMLCOUNT ".th {\n";
829 print HTMLCOUNT " font-weight : normal;\n";
830 print HTMLCOUNT " border-style:solid; \n";
831 print HTMLCOUNT " border-color:white;\n";
832 print HTMLCOUNT " border-width:0px;\n";
833 print HTMLCOUNT " font-family:consolas;\n";
834 print HTMLCOUNT " }\n";
835
836 print HTMLCOUNT ".tab2 {\n";
837 print HTMLCOUNT " margin:auto;\n";
838 print HTMLCOUNT " border-collapse: collapse;\n";
839 print HTMLCOUNT " border-style:solid; \n";
840 print HTMLCOUNT " border-width:3px; \n";
841 print HTMLCOUNT " border-color:white;\n";
842 print HTMLCOUNT " }\n";
843
844 print HTMLCOUNT ".tab {\n";
845 print HTMLCOUNT " margin:auto;\n";
846 print HTMLCOUNT " border-collapse: collapse;\n";
847 print HTMLCOUNT " border-width:3px;\n ";
848 print HTMLCOUNT " border-style:solid;\n ";
849 print HTMLCOUNT " border-color:black;\n";
850 print HTMLCOUNT " }\n";
851
852 print HTMLCOUNT ".td1 { \n";
853 print HTMLCOUNT " border-color:black;\n";
854 print HTMLCOUNT " font-size: 11pt;\n";
855 print HTMLCOUNT " font-family: calibri;\n";
856 print HTMLCOUNT " border-width:1px;\n";
857 print HTMLCOUNT " border-left:3px;\n";
858 print HTMLCOUNT " border-right:3px;\n";
859 print HTMLCOUNT " border-style:solid; \n";
860 print HTMLCOUNT " background-color : #c6c3bd; \n";
861 print HTMLCOUNT " }\n";
862
863 print HTMLCOUNT ".td2 { \n";
864 print HTMLCOUNT " border-color:black;\n";
865 print HTMLCOUNT " font-size: 11pt;\n";
866 print HTMLCOUNT " font-family: calibri;\n";
867 print HTMLCOUNT " border-width:1px;\n";
868 print HTMLCOUNT " border-left:3px;\n";
869 print HTMLCOUNT " border-right:3px;\n";
870 print HTMLCOUNT " border-style:solid; \n";
871 print HTMLCOUNT " background-color : #c6c3ee; \n";
872 print HTMLCOUNT " }\n";
873
874 print HTMLCOUNT ".td3 { \n";
875 print HTMLCOUNT " border-color:black;\n";
876 print HTMLCOUNT " font-size: 11pt;\n";
877 print HTMLCOUNT " font-weight: bold;\n";
878 print HTMLCOUNT " font-family: calibri;\n";
879 print HTMLCOUNT " border-width:3px;\n";
880 print HTMLCOUNT " border-left:3px;\n";
881 print HTMLCOUNT " border-right:3px;\n";
882 print HTMLCOUNT " border-style:solid; \n";
883 print HTMLCOUNT " background-color : white; \n";
884 print HTMLCOUNT " }\n";
885
886
887 print HTMLCOUNT ".ted { \n";
888 print HTMLCOUNT " border-color:black;\n";
889 print HTMLCOUNT " font-weight : bold;\n";
890 print HTMLCOUNT " background-color : #A19EED; \n";
891 print HTMLCOUNT " }\n";
892
893 print HTMLCOUNT ".ted2 { \n";
894 print HTMLCOUNT " border-color:black;\n";
895 print HTMLCOUNT " font-weight : bold;\n";
896 print HTMLCOUNT " background-color : #9A9D7C; \n";
897 print HTMLCOUNT " }\n";
898
899 print HTMLCOUNT ".ted3 { \n";
900 print HTMLCOUNT " border-color:black;\n";
901 print HTMLCOUNT " font-family: calibri;\n";
902 print HTMLCOUNT " color: white;\n";
903 print HTMLCOUNT " background-color : #333333; \n";
904 print HTMLCOUNT " }\n";
905
906 print HTMLCOUNT ".auto-style1 {";
907 print HTMLCOUNT " font-weight: normal;";
908 print HTMLCOUNT " font-size: x-small;";
909 print HTMLCOUNT "}";
910
911 print HTMLCOUNT "</style>\n";
912
913 ###################################################################################################################################################################################
914
915 print HTMLSNP "</head>\n";
916
917 print HTMLSNP "<center><img src=\"".$REPimages."SNiPloid7.png\" WIDTH=250></center>";
918 if ($poly_poly_analysis == 0) {
919 print HTMLSNP "<center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center>";
920 }
921 print HTMLSNP "<p>\n";
922 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
923 print HTMLCOUNT "</head>\n";
924 print HTMLCOUNT "<table><tr><td class=\"tab2\"><img src=\"".$REPimages."SNiPloid7.png\" WIDTH=250>";
925
926 print HTMLCOUNT "<h3><font face=\"calibri\">Synthesis of the analysis</font></h3></td>";
927 if ($poly_poly_analysis == 0) {
928
929 print HTMLCOUNT "<td class=\"tab2\" width=50></td>";
930 print HTMLCOUNT "<td class=\"tab2\"><table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\">";
931 print HTMLCOUNT "<tr><th>Diploids</th><th>Polyploid</th><th>Identity</th><th>Interpretation</th></tr>";
932 print HTMLCOUNT "<tr><td>[1/2]</td><td>[1]</td><td>!=</td><td><img src=\"".$REPimages."1.png\" height=30></td></tr>";
933 print HTMLCOUNT "<tr><td>[1/2]</td><td>[2]</td><td>!=</td><td><img src=\"".$REPimages."2.png\" height=30></td></tr>";
934 print HTMLCOUNT "<tr><td>[1]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."3.png\" height=30></td></tr>";
935 print HTMLCOUNT "<tr><td>[2]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."4.png\" height=30></td></tr>";
936 print HTMLCOUNT "<tr><td>[1/2]</td><td>[1/2]</td><td>=</td><td><img src=\"".$REPimages."5v.png\" height=30></td></tr>";
937 print HTMLCOUNT "<tr><td>[1]</td><td>[2]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>";
938 print HTMLCOUNT "<tr><td>[1]</td><td>[2/3]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>";
939 print HTMLCOUNT "<tr><td>[1/2]</td><td>[2/3]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>";
940 print HTMLCOUNT "<tr><td>[1/2]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30><img src=\"".$REPimages."HG1.png\" height=30></td></tr>";
941 print HTMLCOUNT "<tr><td>[1]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30><img src=\"".$REPimages."HG1.png\" height=30></td></tr>";
942 print HTMLCOUNT "</table></td>";
943 print HTMLCOUNT "<td class=\"tab2\" width=50></td>";
944 print HTMLCOUNT "<td class=\"tab2\"><center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center></td>";
945 #print HTMLCOUNT "<td><table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"><tr><th>Diploids</th><th>Polyploid</th><th>Identity</th><th>Interpretation</th></tr></table></td>";
946 print HTMLCOUNT "</tr></table>";
947 }
948 print HTMLCOUNT "<p>\n";
949 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
950
951 print HTMLSNP "<body>\n";
952
953 if ($poly_poly_analysis == 1) {
954 print HTMLSNP "<center><h3><font face=\"calibri\">Result of SNP comparison of two Polyploids</font></h3></center>";
955 }
956 else {
957 print HTMLSNP "<center><h3><font face=\"calibri\">Result of SNP comparison of a Polyploid and its Parental Genomes (Genome 1 and Genome 2 as reference)</font></h3></center>";
958 }
959
960 print HTMLSNP "<p>\n";
961
962 # COLUMNS - HTMLSNP SNP VIEW
963 print HTMLSNP "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n";
964 print HTMLSNP "<tr>\n";
965 print HTMLSNP "<th>Gene</th>"; # (1) Gene
966 print HTMLSNP "<th>Position</th>"; # (2) Position
967
968 if ($poly_poly_analysis == 1) {
969 print HTMLSNP "<th>REF<br></th>";
970 print HTMLSNP "<th>Polyploid 1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (3) Polyploid
971 print HTMLSNP "<th>Polyploid 2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (4) Polyploid 2
972
973 print HTMLSNP "<th>[Filtered/Total] Depth<br>Polyploid 1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (8) Filtered Depth
974 print HTMLSNP "<th>[Filtered/Total] Depth<br>Polyploid 2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (9) Total Depth
975
976 # Entête fichier SNP VIEW TAB
977 print TABSNP "Gene\t"; # (1) Gene
978 print TABSNP "Position\t"; # (2) Position
979 print TABSNP "REF\t"; # (2) Position
980 print TABSNP "Polyploid 1: ".$polyploidName."\t"; # (3) Polyploid
981 print TABSNP "Polyploid 2: ".$genome1Name."\t"; # (4) Genome 1
982 print TABSNP "P1 Filtered Depth\t"; # (9) Filtered Depth
983 print TABSNP "P1 Total Depth\t"; # (10) Total Depth
984 print TABSNP "P2 Filtered Depth\t"; # (9) Filtered Depth
985 print TABSNP "P2 Total Depth\n"; # (10) Total Depth
986 }
987 else {
988 # (3) Reference
989 print HTMLSNP "<th>Polyploid<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (3) Polyploid
990 print HTMLSNP "<th>Genome 1<br><span class=\"auto-style1\">".$genome1Name."</span></th>"; # (4) Genome 1
991 print HTMLSNP "<th>Genome 2<br><span class=\"auto-style1\">".$genome2Name."</span></th>"; # (5) Genome 2
992 print HTMLSNP "<th>Validation</th>";
993 print HTMLSNP "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>"; # (7) Ratio
994 print HTMLSNP "<th>Filtered<br>Depth</th>"; # (8) Filtered Depth
995 print HTMLSNP "<th>Total<br>Depth</th>"; # (9) Total Depth
996
997 # Entête fichier SNP VIEW TAB
998 print TABSNP "Gene\t"; # (1) Gene
999 print TABSNP "Position\t"; # (2) Position
1000 print TABSNP "Polyploid: ".$polyploidName."\t"; # (3) Polyploid
1001 print TABSNP "Genome 1: ".$genome1Name."\t"; # (4) Genome 1
1002 print TABSNP "Genome 2: ".$genome2Name."\t"; # (5) Genome 2
1003 print TABSNP "Validation\t"; # (6) Validation
1004 print TABSNP "Ratio (%) ".$genome2Name."\t"; # (7) Ratio Genome 1
1005 print TABSNP "Ratio (%) ".$genome1Name."\t"; # (8) Ratio Genome 2
1006 print TABSNP "Filtered Depth\t"; # (9) Filtered Depth
1007 print TABSNP "Total Depth\n"; # (10) Total Depth
1008 }
1009 print HTMLSNP "</tr>\n";
1010
1011
1012
1013 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
1014 print HTMLCOUNT "<body>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n";
1015 print HTMLCOUNT "<p>\n";
1016 # COLUMNS - HTML SYNTHESIS
1017 print HTMLCOUNT "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n";
1018 print HTMLCOUNT "<tr>\n";
1019 print HTMLCOUNT "<th>Gene</th>"; # (1) Gene
1020 print HTMLCOUNT "<th>Interval Size<br>Analysed (pb)</th>"; # (2) Interval Size Analyzed
1021 print HTMLCOUNT "<th>nb Positions<br>with SNP</th>";
1022 if ($poly_poly_analysis == 0) { # (3) nB Positions With SNP
1023 print HTMLCOUNT "<th><img src=\"".$REPimages."1.png\" height=30></th>"; # (4) [1]
1024 print HTMLCOUNT "<th><img src=\"".$REPimages."2.png\" height=30></th>"; # (5) [2]
1025 print HTMLCOUNT "<th><img src=\"".$REPimages."3ou4.png\" height=30></th>"; # (6) [3 or 4]
1026 print HTMLCOUNT "<th><img src=\"".$REPimages."3.png\" height=30></th>"; # (6) [3 or 4]
1027 print HTMLCOUNT "<th><img src=\"".$REPimages."4.png\" height=30></th>"; # (6) [3 or 4]
1028 print HTMLCOUNT "<th><img src=\"".$REPimages."5v.png\" height=30></th>"; # (11) [5]
1029 print HTMLCOUNT "<th><img src=\"".$REPimages."other.png\" height=30></th>"; # (7) [other]
1030 print HTMLCOUNT "<th><img src=\"".$REPimages."HG1.png\" height=30><br><span class=\"auto-style1\">".$genome1Name."</span></th>"; # (8) Heterozygosity For Genome 1
1031 print HTMLCOUNT "<th>SNP Intra-Diploids <br><img src=\"".$REPimages."5v.png\" height=30> + <img src=\"".$REPimages."1.png\" height=30> + <img src=\"".$REPimages."2.png\" height=30> + <img src=\"".$REPimages."other.png\" height=30></th>"; # (9) SNP Diploids
1032 print HTMLCOUNT "<th>SNP Intra-Polyploid <br> <img src=\"".$REPimages."5v.png\" height=30> + <img src=\"".$REPimages."3ou4.png\" height=30> + <img src=\"".$REPimages."other.png\" height=30></th>"; # (10) SNP Polyploid
1033 print HTMLCOUNT "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>\n\n\n\n\n\n\n\n"; # (12) Ratio %
1034
1035 print HTMLCOUNT "</tr>\n";
1036 # Entête HTMLSNP Synthesis
1037 print TABCOUNT "Gene\t"; # (1) Gene
1038 print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb)
1039 print TABCOUNT "nb SNP positions\t"; # (3) nb SNP positions
1040 print TABCOUNT "1\t"; # (4) [1]
1041 print TABCOUNT "2\t"; # (5) [2]
1042 print TABCOUNT "3 or 4\t"; # (6) [3 or 4]
1043 print TABCOUNT "3\t"; # (6) [3 or 4]
1044 print TABCOUNT "4\t"; # (6) [3 or 4]
1045 print TABCOUNT "5\t"; # (11) [5]
1046 print TABCOUNT "other\t"; # (7) [other]
1047 print TABCOUNT "SNP Heterozygosity Genome 1\t"; # (8) SNP Heterozygosity Genome 1
1048 print TABCOUNT "SNP Diploids\t"; # (9) SNP Diploids
1049 print TABCOUNT "SNP Polyploid\t"; # (10) SNP Polyploid
1050 print TABCOUNT "Ratio (%) ".$genome2Name."\t"; # (12) Ratio (%) Genome 2
1051 print TABCOUNT "Ratio (%) ".$genome1Name."\n"; # (13) Ratio (%) Genome 1
1052 }
1053 else {
1054 print HTMLCOUNT "<th>P1 = P2<br><span style=\"font-weight: normal\"><span style=\"background:#DE8A8A\">[1/2]</span> vs <span style=\"background:#DE8A8A\">[1/2]</span></span></th>"; # (4) [1]
1055 print HTMLCOUNT "<th>P1 = P2<br><span style=\"font-weight: normal\"><span style=\"background:#5CAAD2\">[1]</span> vs <span style=\"background:#5CAAD2\">[1]</span></span></th>"; # (4) [1]
1056 print HTMLCOUNT "<th>SNP<br>interpolyploids<br>P1 &ne; P2<br><span style=\"auto-style1\"></span></th>"; # (4) [1] #DE8A8A
1057 print HTMLCOUNT "<th>P1 &ne; P2<br>2 Alleles<br><span style=\"font-weight: normal\"><span style=\"background:#5CAAD2\">[1]</span> vs <span style=\"background:#5CAAD2\">[2]</span></span></th>"; # (4) [1]
1058 print HTMLCOUNT "<th>P1 &ne; P2<br>2 Alleles<br><span style=\"font-weight: normal\"><span style=\"background:#DE8A8A\">[1/2]</span> vs <span style=\"background:#5CAAD2\">[1]</span> or <span style=\"background:#5CAAD2\">[2]</span></span></th>"; # (4) [1]
1059 print HTMLCOUNT "<th>P1 &ne; P2<br>3 Alleles<br><span style=\"font-weight: normal\"><span style=\"background:#DE8A8A\">[1/2]</span> vs <span style=\"background:#5CAAD2\">[3]</span></span></th>"; # (4) [1]
1060 print HTMLCOUNT "<th>P1 &ne; P2<br>3 Alleles<br><span style=\"font-weight: normal\"><span style=\"background:#DE8A8A\">[1/2]</span> vs <span style=\"background:#DE8A8A\">[1/3]</span></span></th>"; # (4) [1]
1061 print HTMLCOUNT "<th>SNP<br>intra P1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (4) [1]
1062 print HTMLCOUNT "<th>SNP<br>intra P2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (4) [1]
1063
1064 print HTMLCOUNT "</tr>\n";
1065 # Entête HTMLSNP Synthesis
1066 print TABCOUNT "Gene\t"; # (1) Gene
1067 print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb)
1068 print TABCOUNT "nb positions with SNP\t"; # (3) nb SNP positions
1069 print TABCOUNT "P1 = P2 [1/2] vs [1/2]\t"; # (4) [1]
1070 print TABCOUNT "P1 = P2 [1] vs [1]\t"; # (4) [1]
1071 print TABCOUNT "SNP interpolyploids P1 diff P2\t"; # (4) [1] #DE8A8A
1072 print TABCOUNT "P1 diff P2 2 Alleles [1] vs [2]\t"; # (4) [1]
1073 print TABCOUNT "P1 diff P2 2 Alleles [1/2] vs [1] or [2]\t"; # (4) [1]
1074 print TABCOUNT "P1 diff P2 3 Alleles [1/2] vs [3]\t"; # (4) [1]
1075 print TABCOUNT "P1 diff P2 3 Alleles [1/2] vs [1/3]\t"; # (4) [1]
1076 print TABCOUNT "SNP intra P1 ".$polyploidName."\t" ; # (4) [1]
1077 print TABCOUNT "SNP intra P2 ".$polyploid2Name."\n" ; # (4) [1]
1078
1079 }
1080 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
1081 $ligneInter = 0 ;
1082 $totalSNP = 0 ;
1083 $totalSize = 0 ;
1084
1085 $total11 = 0 ;
1086 $total22 = 0 ;
1087 $total3ou4 = 0 ;
1088 $total5 = 0 ;
1089 $total512 = 0 ;
1090 $total534 = 0 ;
1091 $totalOther = 0 ;
1092 $totalGenome2 = 0 ;
1093
1094 $total3 = 0 ;
1095 $total4 = 0 ;
1096
1097 $totalNbPolyploid1 = 0 ; # SNP heterozygosity for P1
1098 $totalNbPolyploid2 = 0 ; # SNP heterozygosity for P2
1099 $totalNbCommuns = 0 ; # SNP heterozygosity [P1] = [P2]
1100 $totalNbCommunsHomo = 0 ; # SNP homozygosity [P1] = [P2]
1101 $totalNbDifferent = 0 ; # [P1] ne [P2]
1102 $totalNbHomoDiff = 0 ; # Example : P1 = [A] ; P2 = [G]
1103 $totalNbAlleleCommun = 0 ; # Example : P1 = [A/G] ; P2 = [A]
1104 $totalAlleleDifferent = 0 ; # Example : P1 = [A/G] ; P2 = [C] or [T]
1105 $totalAlleleCommunH = 0 ; # Example : P1 = [A/G] ; P2 = [A/C]
1106
1107 }
1108
1109 sub int_output { # intern reference
1110
1111 foreach my $s(sort(keys(%snp_final))){
1112 #######################################
1113 if ($ligneInter == 0) {
1114 print HTMLSNP "<tr class=\"bord1\">\n";
1115 print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n";
1116 }
1117 else {
1118 print HTMLSNP "<tr class=\"bord2\">\n";
1119 print HTMLCOUNT "<tr class=\"td2\">\n";
1120 }
1121 #######################################
1122
1123 my $ref = $snp_final{$s};
1124 my %hash = %$ref;
1125 $taille = keys(%hash);
1126
1127 # taille de la ligne gene
1128 print HTMLSNP "<td rowspan=\"".$taille."\"><b>".$s."</b></td>";
1129
1130 $ligneOK = 0 ;
1131
1132 $nbPolyploid = 0;
1133 $nbGenomes = 0 ;
1134 $nbGenome2 = 0 ; # SNP chez les diploides dans un cas "Other" avec genome 1 heterozygote
1135 $nbCommuns = 0;
1136 $nbPoly_only = 0 ;
1137 $nbSub_only = 0 ;
1138
1139 $case5 = 0 ;
1140 $case1 = 0 ;
1141 $case2 = 0 ;
1142 $case3ou4 = 0;
1143 $case3 = 0 ;
1144 $case4 = 0 ;
1145 $caseOther = 0;
1146 $casePolyplother = 0 ; # SNP chez le polyploide dans un cas "Other"
1147 $caseDiplother = 0 ; # SNP chez les diploides dans un cas "Other"
1148
1149
1150
1151 # Moyenne Ponderee
1152 $moyenneSNPindep1 = 0 ;
1153 $moyenneSNPindep2 = 0 ;
1154
1155 @tabTrie = sort ({ $a <=> $b }keys %hash);
1156
1157 #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) {
1158 foreach my $c(@tabTrie) {
1159 if ($ligneOK == 1) {
1160 if ($ligneInter == 0) {
1161 print HTMLSNP "<tr class=\"td1\">\n";
1162 }
1163 else {
1164 print HTMLSNP "<tr class=\"td2\">\n";
1165 }
1166 }
1167 ################################################################################
1168 ### Recuperation des informations ###
1169
1170 ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp_final{$s}{$c});
1171 ($DP_P, $FDP) = split(/-/, $DP_P);
1172 #print STDOUT "\n($code_snp:$GT_poly) - ($code_G1:$GT_G1)" ;
1173 if ($GT_poly ne "") { # Polyploide = [0.0] ou [0.1] ou [1.1]
1174 @recupAlleles = split(/\[/,$code_snp);
1175 @recupAlleles = split(/\]/,$recupAlleles[1]);
1176 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
1177 # Attribution des alleles au polyploide si pas de SNP
1178 if ($GT_poly =~ /^0.0$/) { $code_snp = $alRef ; }
1179 if ($GT_poly =~ /^1.1$/) { $code_snp = $alAltP ; }
1180 # Attribution des alleles au genome 1 si pas de SNP
1181 if (($GT_G1 eq "") || ($GT_G1 =~ /^0.0$/)) { $code_G1 = $alRef ; }
1182 if ($GT_G1 =~ /^1.1$/) {
1183 @recupAlleles = split(/\[/,$code_G1);
1184 @recupAlleles = split(/\]/,$recupAlleles[1]);
1185 ($alRef,$alAlt) = split(/\//,$recupAlleles[0]);
1186 $code_G1 = $alAlt;
1187 }
1188 }
1189 elsif ($GT_G1 ne "") { # pas de SNP polyploide dans le fichier 1 (fichiers non mergés) -> equivalent de [0.0]
1190 @recupAlleles = split(/\[/,$code_G1);
1191 @recupAlleles = split(/\]/,$recupAlleles[1]);
1192 ($alRef,$alAlt) = split(/\//,$recupAlleles[0]);
1193 # Attribution des Alleles au genome 1
1194 if ($GT_G1 =~ /^1.1$/) { $code_G1 = $alAlt ; }
1195 if ($GT_G1 =~ /^0.0$/) { $code_G1 = $alRef ; }
1196 }
1197
1198 ################################################################################
1199 $noSNPpoly = "ok" ;
1200
1201
1202
1203
1204 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) {
1205 if ($ligneInter == 0) {
1206 print HTMLSNP "<td class=\"tedG2\">".$c."</td>";
1207 print HTMLSNP "<td class=\"ted2\">".$code_snp."</td>";
1208 print HTMLSNP "<td class=\"ted2\">".$code_G1."</td>";
1209 print HTMLSNP "<td class=\"ted2\">".$alRef."</td>"; #REF
1210 print HTMLSNP "<td class=\"ted2\">OK</td>";
1211
1212 }
1213 else {
1214 print HTMLSNP "<td class=\"tedG\">".$c."</td>";
1215 print HTMLSNP "<td class=\"ted\">".$code_snp."</td>";
1216 print HTMLSNP "<td class=\"ted\">".$code_G1."</td>";
1217 print HTMLSNP "<td class=\"ted\">".$alRef."</td>"; #REF
1218 print HTMLSNP "<td class=\"ted\">OK</td>";
1219 }
1220 }
1221 else {
1222 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
1223 print HTMLSNP "<td>".$code_snp."</td>";
1224 print HTMLSNP "<td>".$code_G1."</td>";
1225 print HTMLSNP "<td>".$alRef."</td>"; #REF
1226 print HTMLSNP "<td></td><td></td><td></td><td></td>";
1227 }
1228 print TABSNP $s."\t".$c."\t".$code_snp."\t".$code_G1."\t".$alRef."\t";
1229
1230
1231
1232 $tailleImg = 35 ;
1233
1234
1235 if (($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) { # SNP POLYPLOID - [0/1] [0|1] [1|0]
1236 # Moyenne du Ratio -----------------------------------
1237 ($sub1,$sub2) = split(",",$ratio);
1238 $somme = $sub1 + $sub2 ;
1239
1240 if ($somme == 0 ) {
1241 print STDOUT "ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"";
1242 die ("ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"");
1243 }
1244 else {
1245 $ratio = ($sub1/($sub1+$sub2))*100;
1246 $ratio = sprintf("%.0f", $ratio);
1247 }
1248 #$ratio = sprintf("%.0f", $ratio);
1249 $ratio2 = 100-$ratio ;
1250
1251 #-----------------------------------------------------
1252 if (($GT_G1 =~ /^1.1$/)){ # Pas de SNP Genome1 [1/1] [1|1] SNP entre genome1 et genome2
1253 if ($code_G1 eq $alAltP) { # 5
1254 $moyenneSNPindep1 = $moyenneSNPindep1 + $ratio ;
1255 $moyenneSNPindep2 = $moyenneSNPindep2 + $ratio2 ;
1256 if ($ligneInter == 0) {
1257 print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO %
1258 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
1259 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2
1260 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>";
1261 print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>";
1262 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=".$tailleImg."></td>";
1263
1264 }
1265 else {
1266 print HTMLSNP "<td class=\"ted\">".$ratio.":".$ratio2."<br>"; # RATIO %
1267 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
1268 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2.">"; # IMG RATIO 2
1269 print HTMLSNP "<td class=\"ted\">".$FDP."</td>";
1270 print HTMLSNP "<td class=\"ted\">".$DP_P."</td>";
1271 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=".$tailleImg."></td>";
1272
1273 }
1274 print TABSNP "OK\t".$ratio."\t".$ratio2."\t".$FDP."\t".$DP_P."\t5";
1275 $case5 ++ ;
1276 }
1277 else { # Other 0.1 - 1.1 (O GA A) # Other [SNP DIPLO + SNP POLY]
1278 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
1279 print TABSNP "\t\t\t\t\tother";
1280 $caseOther ++ ;
1281 $casePolyplother ++ ;
1282 $caseDiplother ++ ;
1283 }
1284 }
1285 else {
1286 if (($GT_G1 =~ /^0.0$/)||($GT_G1 =~ /^$/)){ # 3 ou 4
1287
1288 ###############################################################################################
1289 # PHASING
1290 ###############################################################################################
1291 $phasedornot = 0 ;
1292 if ($GT_poly =~/\|/){
1293
1294 #print STDOUT $s."\n";
1295 my $ref = $phased_regions{$s};
1296 my %hash = %$ref ;
1297 foreach my $num_reg(sort(keys(%hash))){
1298 if (exists $phased_regions{$s}{$num_reg}{$c}) {
1299 $genotype = $phased_regions{$s}{$num_reg}{$c} ;
1300 my $ref2 = $phased_regions{$s}{$num_reg};
1301 my %hash2 = %$ref2 ;
1302 foreach my $pos(sort(keys(%hash2))){
1303 if (exists $five{$s}{$pos}){
1304 if (($five{$s}{$pos} =~ /0.1/ && $GT_poly =~ /0.1/) or ($five{$s}{$pos} =~ /1.0/ && $GT_poly =~ /1.0/)){
1305 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3.png\" height=".$tailleImg."></td>";
1306 $case3 ++ ;
1307 }
1308 else {
1309 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."4.png\" height=".$tailleImg."></td>";
1310 $case4 ++ ;
1311 }
1312 $phasedornot = 1 ;
1313 last ;
1314 }
1315 }
1316 }
1317 }
1318 #print STDOUT "\n";
1319 }
1320 if ($phasedornot == 0) {
1321 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=".$tailleImg."></td>";
1322 $case3ou4 ++ ;
1323 }
1324
1325 ###############################################################################################
1326
1327
1328
1329
1330 print TABSNP "\t\t\t\t\t3or4";
1331
1332 }
1333 else { #0/1 # heterozygosity G1
1334 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>";
1335 print TABSNP "\t\t\t\t\tother,heterozygosity for genome 1";
1336 $nbGenome2 ++ ;
1337 $casePolyplother ++ ;
1338 $caseOther ++ ;
1339 }
1340 }
1341 }
1342
1343 if (($GT_poly =~ /^1.1$/)) { # POLYPLOID NE REFERENCE - [1/1]
1344 if ($GT_G1 && ($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0]
1345 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>";
1346 print TABSNP "\t\t\t\t\tother,heterozygosity for genome 1";
1347 $nbGenome2 ++ ;
1348 $caseOther ++ ;
1349 }
1350 elsif (!$GT_G1){ # POLYPLOID A/A DIPLOIDS T/T
1351 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
1352 print TABSNP "\t\t\t\t\tother";
1353 $caseOther ++ ;
1354 }
1355
1356 else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2
1357 if ($GT_G1 =~ /^0.0$/){ # Other [NOTHING]
1358 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
1359 print TABSNP "\t\t\t\t\tother";
1360 $caseOther ++ ;
1361 }
1362 else {
1363 if ($code_G1 eq $alAltP) { # 2
1364 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=".$tailleImg."></td>";
1365 print TABSNP "\t\t\t\t\t2";
1366 $case2 ++ ;
1367 }
1368 else { # Other [SNP DIPLO]
1369 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
1370 print TABSNP "\t\t\t\t\tother";
1371 $caseOther ++ ;
1372 $caseDiplother ++ ;
1373 }
1374 }
1375 }
1376 }
1377
1378 if (($GT_poly =~ /^0.0$/)||($GT_poly =~ /^$/)) { #POLYPLOID == REFERENCE - [0|0]
1379 ####################################
1380 if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0]
1381 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>";
1382 print TABSNP "\t\t\t\t\tother,heterozygosity for genome 1";
1383 $nbGenome2 ++ ;
1384 $caseOther++;
1385 }
1386 else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2
1387 if ($GT_G1 =~ /^1.1$/){
1388 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=".$tailleImg."></td>";
1389 print TABSNP "\t\t\t\t\t1";
1390 $case1 ++ ;
1391 }
1392 }
1393 }
1394
1395 print TABSNP "\n";
1396 print HTMLSNP "</tr>\n";
1397 $ligneOK = 1 ;
1398 }
1399
1400 if ($ligneInter == 0) {
1401 print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">".$s."</td>";
1402 }
1403 else {
1404 print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">".$s."</td>";
1405 }
1406 print TABCOUNT $s."\t";
1407
1408 #######################################
1409 if ($ligneInter == 0) { $ligneInter = 1 ; }
1410 else { $ligneInter = 0 ; }
1411 #######################################
1412
1413 # Calcul des intervalles #
1414 ##########################
1415 $taille_totale = 0 ;
1416 my $ref = $intervalle2{$s};
1417 my %hash = %$ref;
1418
1419 foreach my $interval(keys(%hash)){
1420 my @pos = split(/-/,$interval);
1421 $taille_inter = $pos[1]-$pos[0]+1 ;
1422 $taille_totale = $taille_totale + $taille_inter;
1423 }
1424 $total1 = $case5 + $case1 + $case2 + $caseDiplother + $nbGenome2;
1425 $total2 = $case5 + $case3ou4 + $casePolyplother;
1426
1427
1428
1429 # SYNTHESIS
1430 print HTMLCOUNT "<td>".$taille_totale."</td><td style=\"border-left:3px solid black\">".$taille."</td></td>";
1431 print HTMLCOUNT "<td style=\"border-left:3px solid black\">";
1432 print HTMLCOUNT $case1."</td><td>".$case2."</td><td>".$case3ou4."</td><td>";
1433 print HTMLCOUNT $case3."</td><td>".$case4."</td><td>".$case5."</td><td>";
1434 print HTMLCOUNT $caseOther."</td><td style=\"border-left:3px solid black\">".$nbGenome2."</td><td style=\"border-left:3px solid black\">".$total1."</td>";
1435 print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$total2."</td>";
1436 print TABCOUNT $taille_totale."\t".$taille."\t";
1437 print TABCOUNT $case1."\t".$case2."\t".$case3ou4."\t".$case3."\t".$case4."\t".$case5."\t".$caseOther."\t".$nbGenome2."\t".$total1."\t".$total2."\t";
1438
1439 $nbTotGenesAna ++ ;
1440
1441 if ($case5 != 0) {
1442 $nbTotGenesVal ++ ;
1443 if ($ligneInter == 1) {
1444 print HTMLCOUNT "<td class=\"ted2\" style=\"border-left:3px solid black\">";
1445 print HTMLCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."<br>";
1446 print HTMLCOUNT "<img src=\"".$REPimages."r1.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep1/$case5).">";
1447 print HTMLCOUNT "<img src=\"".$REPimages."r2.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep2/$case5)."></td>";
1448 }
1449 else {
1450 print HTMLCOUNT "<td class=\"ted\" style=\"border-left:3px solid black\">";
1451 print HTMLCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."<br>";
1452 print HTMLCOUNT "<img src=\"".$REPimages."r1.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep1/$case5).">";
1453 print HTMLCOUNT "<img src=\"".$REPimages."r2.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep2/$case5)."></td>";
1454 }
1455 print TABCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5)."\t".sprintf("%.0f", $moyenneSNPindep2/$case5)."\t";
1456 }
1457 else {
1458 print HTMLCOUNT "<td style=\"border-left:3px solid black\"></td>";
1459 print TABCOUNT "\t";
1460 }
1461 print HTMLCOUNT "</tr>";
1462 print TABCOUNT "\n";
1463
1464 $totalSize = $totalSize + $taille_totale ;
1465 $totalSNP = $totalSNP + $taille ;
1466 $total11 = $total11 + $case1 ;
1467 $total22 = $total22 + $case2 ;
1468 $total3ou4 = $total3ou4 + $case3ou4 ;
1469 $total3 = $total3 + $case3 ;
1470 $total4 = $total4 + $case4 ;
1471 $total5 = $total5 + $case5 ;
1472 $total512 = $total512 + $total1 ;
1473 $total534 = $total534 + $total2 ;
1474 $totalOther = $totalOther + $caseOther ;
1475 $totalGenome2 = $totalGenome2 + $nbGenome2 ;
1476 }
1477 ########## MODIF DERNIERE MINUTE ################"
1478 print HTMLCOUNT "<tr class=\"td3\">\n<td>";
1479
1480 print HTMLCOUNT $nbTotGenesAna."<td style=\"border-left:3px solid black\">";
1481 print HTMLCOUNT $totalSize."</td><td style=\"border-left:3px solid black\">";
1482 print HTMLCOUNT $totalSNP."</td><td style=\"border-left:3px solid black\">";
1483 print HTMLCOUNT $total11."</td><td>";
1484 print HTMLCOUNT $total22."</td><td>";
1485 print HTMLCOUNT $total3ou4."</td><td>";
1486 print HTMLCOUNT $total3."</td><td>";
1487 print HTMLCOUNT $total4."</td><td>";
1488 print HTMLCOUNT $total5."</td><td>";
1489 print HTMLCOUNT $totalOther."</td><td style=\"border-left:3px solid black\">";
1490 print HTMLCOUNT $totalGenome2."</td><td style=\"border-left:3px solid black\">";
1491 print HTMLCOUNT $total512."</td><td style=\"border:3px solid black\">";
1492 print HTMLCOUNT $total534."</td><td style=\"border:3px solid black\">";
1493
1494 print HTMLCOUNT $nbTotGenesVal."</td>";
1495
1496 print HTMLCOUNT "</tr>";
1497
1498
1499 print TABCOUNT "$nbTotGenesAna\t$totalSize\t$totalSNP\t$total11\t$total22\t$total3ou4\t$total3\t$total4\t$total5\t$totalOther\t$totalGenome2\t$total512\t$total534\t";
1500 print TABCOUNT "\n";
1501
1502 ####################################################
1503 print HTMLSNP "</table>\n";
1504 print HTMLSNP "</html>\n";
1505 close HTMLSNP ;
1506
1507 print HTMLCOUNT "</table>\n";
1508 print HTMLCOUNT "</html>\n";
1509 close HTMLCOUNT ;
1510
1511 close TABSNP;
1512 close TABCOUNT ;
1513
1514 tie @array, 'Tie::File', $SNP_count or die ;
1515
1516 $array[113] = "<tr><td class=\"ted3\">".$nbTotGenesAna."</td><td class=\"ted3\" style=\"border-left:3px solid black\">".$totalSize."</td><td class=\"ted3\" style=\"border-left:3px solid black\">".$totalSNP."</td></td>";
1517 $array[114] = "<td class=\"ted3\" style=\"border-left:3px solid black\">";
1518 $array[115] = $total11."</td><td class=\"ted3\">".$total22."</td><td class=\"ted3\">".$total3ou4."</td><td class=\"ted3\">";
1519 $array[116] = $total3."</td><td class=\"ted3\">".$total4."</td><td class=\"ted3\">".$total5."</td><td class=\"ted3\">";
1520 $array[117] = $totalOther."</td><td class=\"ted3\" style=\"border-left:3px solid black\">".$totalGenome2."</td><td class=\"ted3\" style=\"border-left:3px solid black\">".$total512."</td>";
1521 $array[118] = "<td class=\"ted3\" style=\"border-left:3px solid black\">".$total534."</td><td class=\"ted3\">".$nbTotGenesVal."</td></tr>";
1522 }
1523 sub ext_output { # Extern reference
1524
1525 print TABCOUNT "Gene;Interval Size Analysed (pb);nb SNP;1;2;3 or 4;5;other;SNP Diploids;SNP Polyploid;Ratio (%) $genome2Name:$genome1Name\n";
1526
1527 foreach my $s(sort(keys(%snp))){
1528
1529 #######################################
1530 if ($ligneInter == 0) {
1531 print HTMLSNP "<tr class=\"bord1\">\n";
1532 print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n";
1533 }
1534 else {
1535 print HTMLSNP "<tr class=\"bord2\">\n";
1536 print HTMLCOUNT "<tr class=\"td2\">\n";
1537 }
1538 #######################################
1539
1540
1541 my $ref = $snp{$s};
1542 my %hash = %$ref;
1543 $taille = keys(%hash);
1544 # taille de la ligne gene
1545 print HTMLSNP "<td rowspan=\"$taille\"><b>$s</b></td>";
1546
1547 $ligneOK = 0 ;
1548
1549 $nbPolyploid = 0;
1550 $nbGenomes = 0 ;
1551 $nbCommuns = 0;
1552 $nbPoly_only = 0 ;
1553 $nbSub_only = 0 ;
1554
1555 $case5 = 0 ;
1556 $case1 = 0 ;
1557 $case2 = 0 ;
1558 $case3ou4 = 0;
1559 $caseOther = 0;
1560 $caseGenome2 = 0 ;
1561
1562 #Moyenne Ponderee
1563 $moyenneSNPindep1 = 0 ;
1564 $moyenneSNPindep2 = 0 ;
1565
1566 @tabTrie = sort ({ $a <=> $b }keys %hash);
1567
1568 #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) {
1569 foreach my $c(@tabTrie) {
1570 $nb1 = 0 ;
1571 $nb2 = 0 ;
1572 $nb3 = 0 ;
1573 if ($ligneOK == 1) {
1574 if ($ligneInter == 0) {
1575 print HTMLSNP "<tr class=\"td1\">\n";
1576 }
1577 else {
1578 print HTMLSNP "<tr class=\"td2\">\n";
1579 }
1580 }
1581 ### Recuperation des informations ###
1582 ($code_snp,$ratio,$GT_poly,$GT_G1,$GT_G2,$DP_P) = split(/\t/,$snp{$s}{$c});
1583 @recupAlleles = split(/\[/,$code_snp);
1584 @recupAlleles = split(/\]/,$recupAlleles[1]);
1585 ($alRef,$alAlt) = split(/\//,$recupAlleles[0]);
1586 $noSNPpoly = "ok" ;
1587
1588 #print STDOUT "\n $c $GT_poly $GT_G1 $GT_G2";
1589 print HTMLSNP "<td>$c</td>";
1590 print TABSNP "$c;";
1591 #####################################################################
1592 # SNP POLYPLOID - [0/1] [0|1] [1|0]
1593 #####################################################################
1594 if (($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^1.0$/) ) { # Polyploid [0.1] [1.0]
1595 $ratio = sprintf("%.0f", $ratio);
1596 $ratio2 = 100-$ratio ;
1597 $moyenneSNPindep1 = $moyenneSNPindep1 + $ratio ;
1598 $moyenneSNPindep2 = $moyenneSNPindep2 + $ratio2 ;
1599 print HTMLSNP "<td>$code_snp</td>";
1600 print TABSNP "$code_snp;";
1601 if (($GT_G1 =~ /^1.1$/)){ # Genome1 [1/1] [1|1]
1602 print HTMLSNP "<td>$alAlt</td>";
1603 print TABSNP "$alAlt;";
1604 if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1]
1605 print HTMLSNP "<td>$alAlt</td>";
1606 print HTMLSNP "<td></td>";
1607 print HTMLSNP "<td></td>";
1608 print HTMLSNP "<td></td>";
1609 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>";
1610 print TABSNP "$alAlt;";
1611 print TABSNP ";";
1612 print TABSNP ";";
1613 print TABSNP ";";
1614 print TABSNP "3 or 4;";
1615 }
1616 else {
1617 if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0]
1618 print HTMLSNP "<td>$alRef</td>";
1619 print HTMLSNP "<td>OK</td>";
1620 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1621 print HTMLSNP "<td></td>";
1622 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
1623 print TABSNP "$alRef";
1624 print TABSNP "OK";
1625 print TABSNP "[$ratio/$ratio2;]";
1626 print TABSNP "$DP_P;";
1627 print TABSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
1628 }
1629 else { # Genome2 = SNP [0.1]
1630 print HTMLSNP "<td>$code_snp</td>";
1631 print HTMLSNP "<td>OK</td>";
1632 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1633 print HTMLSNP "<td></td>";
1634 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
1635 print TABSNP "$code_snp;";
1636 print TABSNP "OK;";
1637 print TABSNP "[$ratio/$ratio2];";
1638 print TABSNP "$DP_P;";
1639 print TABSNP "5';";
1640 }
1641 }
1642 }
1643 else{
1644 if ($GT_G1 =~ /^0.0$/){ # # Genome1 [0/0] [0|0]
1645 print HTMLSNP "<td>$alRef</td>";
1646 print TABSNP "$alRef;";
1647 if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1]
1648 print HTMLSNP "<td>$alAlt</td>";
1649 print HTMLSNP "<td>OK</td>";
1650 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1651 print HTMLSNP "<td></td>";
1652 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
1653 print TABSNP "$alAlt;";
1654 print TABSNP "OK;";
1655 print TABSNP "[$ratio/$ratio2];";
1656 print TABSNP ";";
1657 print TABSNP "5;";
1658 }
1659 else {
1660 if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0]
1661 print HTMLSNP "<td>$alRef</td>";
1662 print HTMLSNP "<td></td>";
1663 print HTMLSNP "<td></td>";
1664 print HTMLSNP "<td></td>";
1665 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>";
1666 print TABSNP "$alRef;";
1667 print TABSNP ";";
1668 print TABSNP ";";
1669 print TABSNP ";";
1670 print TABSNP "3 or 4;";
1671 }
1672 else { # Genome2 = SNP [0.1]
1673 print HTMLSNP "<td>$code_snp</td>";
1674 print HTMLSNP "<td>OK</td>";
1675 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1676 print HTMLSNP "<td></td>";
1677 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
1678 print TABSNP "$code_snp;";
1679 print TABSNP "OK;";
1680 print TABSNP "[$ratio/$ratio2];";
1681 print TABSNP ";";
1682 print TABSNP "5';";
1683 }
1684 }
1685 }
1686 else { # SNP Genome1 [0/1] [0|1] [1|0]
1687 print HTMLSNP "<td>$code_snp</td>"; #REF
1688 print HTMLSNP "$code_snp;"; #REF
1689 if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1]
1690 print HTMLSNP "<td>$alAlt</td>";
1691 print HTMLSNP "<td>OK</td>";
1692 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1693 print HTMLSNP "<td></td>";
1694 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
1695 print TABSNP "$alAlt;";
1696 print TABSNP "OK;";
1697 print TABSNP "[$ratio/$ratio2];";
1698 print TABSNP ";";
1699 print TABSNP "5'";
1700 }
1701 else {
1702 if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0]
1703 print HTMLSNP "<td>$alRef</td>";
1704 print HTMLSNP "<td>OK</td>";
1705 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1706 print HTMLSNP "<td></td>";
1707 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
1708 print TABSNP "$alRef;";
1709 print TABSNP "OK;";
1710 print TABSNP "[$ratio/$ratio2];";
1711 print TABSNP ";";
1712 print TABSNP "5';";
1713 }
1714 else { # Genome2 = SNP [0.1]
1715 print HTMLSNP "<td>$code_snp</td>";
1716 print HTMLSNP "<td></td>";
1717 print HTMLSNP "<td></td>";
1718 print HTMLSNP "<td></td>";
1719 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>";
1720 print TABSNP "$code_snp;";
1721 print TABSNP ";";
1722 print TABSNP ";";
1723 print TABSNP ";";
1724 print TABSNP "5''";
1725 }
1726 }
1727 }
1728 print TABSNP "\n";
1729 $ligneOK = 1 ;
1730 print HTMLSNP "</tr>\n";
1731 }
1732 }
1733 #####################################################################
1734 # POLYPLOID NE REFERENCE - [1/1]
1735 #####################################################################
1736 #print STDOUT "GTPOLY:$GT_poly@";
1737 if (($GT_poly =~ /^1.1$/) ) {
1738 print HTMLSNP "<td>$alAlt</td>";
1739 print TABSNP "$alAlt;";
1740 ####################################
1741 if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # Genome 1 [0/1] [0|1] [1|0]
1742 print HTMLSNP "<td>$code_snp</td>";
1743 print TABSNP "$code_snp";
1744 if ($GT_G2 =~ /^1.1$/) {
1745 print HTMLSNP "<td>$alAlt</td>";
1746 print HTMLSNP "<td></td>";
1747 print HTMLSNP "<td></td>";
1748 print HTMLSNP "<td></td>";
1749 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
1750 print TABSNP "$alAlt;;;;5' or 1;";
1751 }
1752 else {
1753 if ($GT_G2 =~ /^0.0$/) {
1754 print HTMLSNP "<td>$alRef</td>";
1755 print HTMLSNP "<td></td>";
1756 print HTMLSNP "<td></td>";
1757 print HTMLSNP "<td></td>";
1758 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
1759 print TABSNP "$altRef;;;;5' or 1;";
1760 }
1761 else { # Genome2 = SNP [0.1]
1762 print HTMLSNP "<td>$code_snp</td>";
1763 print HTMLSNP "<td></td>";
1764 print HTMLSNP "<td></td>";
1765 print HTMLSNP "<td></td>";
1766 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>";
1767 print TABSNP "$code_snp;;;;5'';";
1768 }
1769 }
1770 }
1771 else {
1772 if ($GT_G1 =~ /^0.0$/){ # Genome1 [0/0] [0|0]
1773 ###################
1774 print HTMLSNP "<td>$alRef</td>";
1775 print TABSNP "$alRef";
1776 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
1777 print HTMLSNP "<td>$alAlt</td>";
1778 print HTMLSNP "<td></td>";
1779 print HTMLSNP "<td></td>";
1780 print HTMLSNP "<td></td>";
1781 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=30></td>";
1782 print TABSNP "$alAlt;;;;1;";
1783 }
1784 else {
1785 if ($GT_G2 =~ /^0.0$/) {
1786 print HTMLSNP "<td>$alAlt</td>";
1787 print HTMLSNP "<td></td>";
1788 print HTMLSNP "<td></td>";
1789 print HTMLSNP "<td></td>";
1790 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>";
1791 print TABSNP "$alAlt;;;;3 or 4;";
1792 }
1793 else { # Genome2 = SNP [0.1]
1794 print HTMLSNP "<td>$code_snp</td>";
1795 print HTMLSNP "<td></td>";
1796 print HTMLSNP "<td></td>";
1797 print HTMLSNP "<td></td>";
1798 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
1799 print TABSNP "$code_snp;;;;5' or 2";
1800 }
1801 }
1802 }
1803 else { # [1/1] [1|1] Genome 1
1804 print HTMLSNP "<td>$alAlt</td>";
1805 print TABSNP "$alAlt";
1806 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
1807 print HTMLSNP "<td>$alAlt</td>";
1808 print HTMLSNP "<td>OK</td>";
1809 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1810 print HTMLSNP "<td>$DP_P</td>";
1811 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
1812 print TABSNP "$alAlt;OK;[$ratio/$ratio2];$DP_P;5;";
1813 }
1814 else {
1815 if ($GT_G2 =~ /^0.0$/) {
1816 print HTMLSNP "<td>$alRef</td>";
1817 print HTMLSNP "<td></td>";
1818 print HTMLSNP "<td></td>";
1819 print HTMLSNP "<td></td>";
1820 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=30></td>";
1821 print TABSNP "$alRef;;;;2;";
1822 }
1823 else { # Genome2 = SNP [0.1]
1824 print HTMLSNP "<td>$code_snp</td>";
1825 print HTMLSNP "<td></td>";
1826 print HTMLSNP "<td></td>";
1827 print HTMLSNP "<td></td>";
1828 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
1829 print TABSNP "$code_snp;;;;5' or 2" ;
1830 }
1831 }
1832 }
1833 }
1834 $nbPolyploid ++ ;
1835 print TABSNP "\n";
1836 $ligneOK = 1 ;
1837 print HTMLSNP "</tr>\n";
1838
1839 }
1840 #####################################################################
1841 # POLYPLOID == REFERENCE - [0|0]
1842 #####################################################################
1843 if (($GT_poly =~ /^0.0$/) ) {
1844 print HTMLSNP "<td>$alRef</td>";
1845 print TABSNP "$alRef;";
1846 if (($GT_G1 !~ /^0.1$/) && ($GT_G1 !~ /^1.0$/)){ # Genome1 intra [0/1] [0|1] [1|0]
1847 print HTMLSNP "<td>$code_snp</td>";
1848 print TABSNP "$code_snp";
1849 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
1850 print HTMLSNP "<td>$alAlt</td>";
1851 print HTMLSNP "<td></td>";
1852 print HTMLSNP "<td></td>";
1853 print HTMLSNP "<td></td>";
1854 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
1855 print TABSNP "$alAlt;;;;5' or 1";
1856 }
1857 else {
1858 if ($GT_G2 =~ /^0.0$/) { # Genome2 = Ref [0.0]
1859 print HTMLSNP "<td>$alRef</td>";
1860 print HTMLSNP "<td></td>";
1861 print HTMLSNP "<td></td>";
1862 print HTMLSNP "<td></td>";
1863 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
1864 print TABSNP "$alRef;;;;5' or 1";
1865 }
1866 else { # Genome2 = SNP [0.1]
1867 if ( ($GT_G2 =~ /^0.1$/) || ($GT_G2 =~ /^1.0$/)){ # Genome2 = SNP [0.1]
1868 print HTMLSNP "<td>$code_snp</td>";
1869 print HTMLSNP "<td></td>";
1870 print HTMLSNP "<td></td>";
1871 print HTMLSNP "<td></td>";
1872 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>";
1873 print TABSNP "$code_snp;;;;5''";
1874 }
1875 }
1876 }
1877 }
1878
1879 else {
1880 if ($GT_G1 =~ /^0.0$/){ # Pas de SNP Genome1 [0/0] [0|0]
1881 print HTMLSNP "<td>$alRef</td>";
1882 print TABSNP "$alRef";
1883 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
1884 print HTMLSNP "<td>$alAlt</td>";
1885 print HTMLSNP "<td></td>";
1886 print HTMLSNP "<td></td>";
1887 print HTMLSNP "<td></td>";
1888 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=30></td>";
1889 print TABSNP "$alAlt;;;;2;";
1890 }
1891 else {
1892 if ( ($GT_G2 =~ /^0.1$/) || ($GT_G2 =~ /^1.0$/)){
1893 print HTMLSNP "<td>$code_snp</td>";
1894 print HTMLSNP "<td>OK</td>";
1895 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
1896 print HTMLSNP "<td>$DP_P</td>";
1897 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
1898 print TABSNP "$code_snp;OK;[$ratio/$ratio2];$DP_P;5' or 2";
1899 }
1900 }
1901 }
1902
1903 else { # [1/1] [1|1] SNP entre genome1 et genome2
1904 print HTMLSNP "<td>$alAlt</td>";
1905 print TABSNP "$alAlt";
1906 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
1907 print HTMLSNP "<td>$alAlt</td>";
1908 print HTMLSNP "<td></td>";
1909 print HTMLSNP "<td></td>";
1910 print HTMLSNP "<td></td>";
1911 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=30></td>";
1912 print TABSNP "$alAlt;;;;other;";
1913 }
1914 else {
1915 if ($GT_G2 =~ /^0.0$/) {
1916 print HTMLSNP "<td>$alRef</td>";
1917 print HTMLSNP "<td></td>";
1918 print HTMLSNP "<td></td>";
1919 print HTMLSNP "<td></td>";
1920 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=30></td>";
1921 print TABSNP "$alRef;;;;1;";
1922 }
1923 else { # Genome2 = SNP [0.1]
1924 print HTMLSNP "<td>$code_snp</td>";
1925 print HTMLSNP "<td></td>";
1926 print HTMLSNP "<td></td>";
1927 print HTMLSNP "<td></td>";
1928 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
1929 print TABSNP "$code_snp;;;;5' or 2;";
1930 }
1931 }
1932 }
1933
1934 }
1935 }
1936 $nbSub_only ++;
1937 print TABSNP "\n";
1938 $ligneOK = 1 ;
1939 print HTMLSNP "</tr>\n";
1940 }
1941
1942 if ($ligneInter == 0) {
1943 print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">$s</td>";
1944 }
1945 else {
1946 print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">$s</td>";
1947 }
1948
1949 print TABCOUNT "Gene;Interval Size;Analysed (pb);nb SNP;1;2;3 or 4;5;5';5'';5' or 1;5'' or 2;other;SNP Diploids;SNP Polyploid;Ratio (%) $genome2Name:$genome1Name;";
1950
1951 #######################################
1952 if ($ligneInter == 0) {
1953 $ligneInter = 1 ;
1954 }
1955 else {
1956 $ligneInter = 0 ;
1957 }
1958 #######################################
1959
1960 # Calcul des intervalles
1961 $taille_totale = 0 ;
1962 my $ref = $intervalle2{$s};
1963 my %hash = %$ref;
1964
1965 foreach my $interval(keys(%hash)){
1966 my @pos = split(/-/,$interval);
1967 $taille_inter = $pos[1]-$pos[0]-1 ;
1968 $taille_totale = $taille_totale + $taille_inter;
1969 }
1970
1971 $total1 = $case5 + $case1 + $case2 ;
1972 $total2 = $case5 + $case3ou4 ;
1973
1974 print HTMLCOUNT "<td>$taille_totale</td><td style=\"border-left:3px solid black\">$taille</td></td>";
1975 print HTMLCOUNT "<td style=\"border-left:3px solid black\">$case1</td><td>$case2</td><td>$case3ou4</td><td>$case5</td><td>$caseGenome2</td><td>$caseOther</td><td style=\"border-left:3px solid black\">$total1</td><td style=\"border-left:3px solid black\">$total2</td>";
1976 if ($case5 != 0) {
1977 print HTMLCOUNT "<td style=\"border-left:3px solid black\">".sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."</td>";
1978 }
1979 else {
1980 print HTMLCOUNT "<td style=\"border-left:3px solid black\"></td>";
1981 }
1982 print HTMLCOUNT "</tr>";
1983
1984 $totalSize = $totalSize + $taille_totale ;
1985 $totalSNP = $totalSNP + $taille ;
1986 $total11 = $total11 + $case1 ;
1987 $total22 = $total22 + $case2 ;
1988 $total3ou4 = $total3ou4 + $case3ou4 ;
1989 $total5 = $total5 + $case5 ;
1990 $total512 = $total512 + $total1 ;
1991 $total534 = $total534 + $total2 ;
1992 $totalOther = $totalOther + $caseOther ;
1993 $totalGenome2 = $totalGenome2 + $caseGenome2 ;
1994 }
1995 ########## MODIF DERNIERE MINUTE ################"
1996 print HTMLCOUNT "<tr class=\"td3\">\n";
1997 print HTMLCOUNT "<td></td><td style=\"border-left:3px solid black\">$totalSize</td><td style=\"border-left:3px solid black\">$totalSNP</td><td style=\"border-left:3px solid black\">$total11</td><td>$total22</td><td>$total3ou4</td><td>$total5</td><td>$totalGenome2</td><td>$totalOther</td><td style=\"border-left:3px solid black\">$total512</td><td style=\"border-left:3px solid black\">$total534</td><td style=\"border-left:3px solid black\"></td>";
1998 print HTMLCOUNT "</tr>";
1999 ####################################################
2000 print HTMLSNP "</table>\n";
2001 print HTMLSNP "</html>\n";
2002 print HTMLCOUNT "</table>\n";
2003 print HTMLCOUNT "</html>\n";
2004
2005 close TABSNP;
2006 close HTMLSNP ;
2007 close HTMLCOUNT ;
2008 }
2009
2010 sub poly_poly_output {
2011 foreach my $s(sort(keys(%snp_final))){
2012 #######################################
2013 if ($ligneInter == 0) {
2014 print HTMLSNP "<tr class=\"bord1\">\n";
2015 print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n";
2016 }
2017 else {
2018 print HTMLSNP "<tr class=\"bord2\">\n";
2019 print HTMLCOUNT "<tr class=\"td2\">\n";
2020 }
2021 #######################################
2022
2023 my $ref = $snp_final{$s};
2024 my %hash = %$ref;
2025 $taille = keys(%hash);
2026
2027 # taille de la ligne gene
2028 print HTMLSNP "<td rowspan=\"".$taille."\"><b>".$s."</b></td>";
2029
2030 $ligneOK = 0 ;
2031
2032 $nbPolyploid1 = 0 ; # SNP heterozygosity for P1
2033 $nbPolyploid2 = 0 ; # SNP heterozygosity for P2
2034 $nbCommuns = 0 ; # SNP heterozygosity [P1] = [P2]
2035 $nbCommunHomo = 0 ; # SNP homozygosity [P1] = [P2]
2036 $nbDifferent = 0 ; # [P1] ne [P2]
2037 $alleleCommun = 0 ; # Example : P1 = [A/G] ; P2 = [A]
2038 $alleleDifferent = 0 ; # Example : P1 = [A/G] ; P2 = [C] or [T]
2039 $alleleCommunH = 0 ; # Example : P1 = [A/G] ; P2 = [A/C]
2040 $nbHomoDiff = 0 ;
2041
2042 @tabTrie = sort ({ $a <=> $b }keys %hash);
2043
2044 $taille = 0;
2045
2046
2047
2048 #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) {
2049 foreach my $c(@tabTrie) {
2050
2051 if ($ligneOK == 1) {
2052 if ($ligneInter == 0) {
2053 print HTMLSNP "<tr class=\"td1\">\n";
2054 }
2055 else {
2056 print HTMLSNP "<tr class=\"td2\">\n";
2057 }
2058 }
2059
2060 #print STDOUT "\n\n\n".$snp_final{$s}{$c} ;
2061 ($code_snp,$AD,$GT_poly,$DP_P,$code_snp2,$AD_2,$GT_poly2,$DP_P2) = split(/\t/,$snp_final{$s}{$c});
2062 ($DP_P, $FDP) = split(/-/, $DP_P);
2063 ($DP_P2, $FDP2) = split(/-/, $DP_P2);
2064
2065 #print STDOUT "\nALLELES :".$AD." - ".$AD_2;
2066
2067 ($sub1_1,$sub1_2) = split(",",$AD);
2068 ($sub2_1,$sub2_2) = split(",",$AD_2);
2069
2070 # $sub1_1 = sprintf("%.0f", $sub1_1);
2071 # $sub1_2 = sprintf("%.0f", $sub1_2);
2072 # $sub2_1 = sprintf("%.0f", $sub2_1);
2073 # $sub2_2 = sprintf("%.0f", $sub2_2);
2074 if ($DP_P > 0) {
2075 $SG1 = ($sub1_1/$DP_P*100) ;
2076 $SG2 = ($sub1_2/$DP_P*100) ;
2077 }
2078 if ($DP_P2 > 0) {
2079 $SG3 = ($sub2_1/$DP_P2*100) ;
2080 $SG4 = ($sub2_2/$DP_P2*100) ;
2081 }
2082
2083
2084 if ($GT_poly ne "") { # Polyploide 1 = [0.0] ou [0.1] ou [1.1]
2085 @recupAlleles = split(/\[/,$code_snp);
2086 @recupAlleles = split(/\]/,$recupAlleles[1]);
2087 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
2088 # Attribution des alleles au polyploide 1 si pas de SNP
2089 if ($GT_poly =~ /^0.0$/) { $code_snp = $alRef ; }
2090 if ($GT_poly =~ /^1.1$/) { $code_snp = $alAltP ; }
2091 # Attribution des alleles au polyploide 2 si pas de SNP
2092 if (($GT_poly2 eq "") || ($GT_poly2 =~ /^0.0$/)) { $code_snp2 = $alRef ; }
2093 if ($GT_poly2 =~ /^1.1$/) {
2094 @recupAlleles = split(/\[/,$code_snp2);
2095 @recupAlleles = split(/\]/,$recupAlleles[1]);
2096 ($alRef,$alAlt2) = split(/\//,$recupAlleles[0]);
2097 $code_snp2 = $alAlt2 ;
2098 }
2099 }
2100 elsif ($GT_poly2 ne "") { # pas de SNP polyploide 1 dans le fichier 1 (fichiers non mergés) -> equivalent de [0.0]
2101 @recupAlleles = split(/\[/,$code_snp2);
2102 @recupAlleles = split(/\]/,$recupAlleles[1]);
2103 ($alRef,$alAlt2) = split(/\//,$recupAlleles[0]);
2104 # Attribution des Alleles au polyploide 2
2105 if ($GT_poly2 =~ /^1.1$/) { $code_snp2 = $alAlt2 ; }
2106 if ($GT_poly2 =~ /^0.0$/) { $code_snp2 = $alRef ; }
2107 }
2108 #print STDOUT "\n($code_snp:$GT_poly) - ($code_snp2:$GT_poly2)" ;
2109 $noSNPpoly = "ok" ;
2110 #____________________________________________________________________________________________________________________________________________
2111 # [1] P1 = 0/1 ; P2 = 0/1 (2 alleles)
2112 #print STDOUT "\n".($code_snp2 eq $code_snp);
2113 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_poly2 =~ /^0.1$/)||($GT_poly2 =~ /^1.0$/))) {
2114
2115 if (($SG1 > $value_filter_p1) && ($SG2 > $value_filter_p1) && ($SG3 > $value_filter_p2) && ($SG4 > $value_filter_p2) && $code_snp2 eq $code_snp) {
2116
2117
2118 if ($ligneInter == 0) {
2119
2120 print HTMLSNP "<td class=\"tedG2\">".$c."</td>";
2121 print HTMLSNP "<td class=\"tedG2\">".$alRef."</td>";
2122 print HTMLSNP "<td class=\"ted2\">".$code_snp."</td>";
2123 print HTMLSNP "<td class=\"ted2\">".$code_snp2."</td>";
2124
2125 print TABSNP $s . "\t";
2126 print TABSNP $c . "\t";
2127 print TABSNP $alRef . "\t";
2128 print TABSNP $code_snp . "\t";
2129 print TABSNP $code_snp2 . "\t";
2130 print TABSNP $FDP."/".$DP_P;
2131
2132 print HTMLSNP "<td class=\"ted2\">".$FDP."/".$DP_P;
2133 if (($DP_P) != 0) {
2134 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2135 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2136 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2137 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2138 }
2139 else {
2140 print HTMLSNP "</td>";
2141 print TABSNP "\t";
2142 }
2143
2144 print TABSNP $FDP2."/".$DP_P2;
2145 print HTMLSNP "<td class=\"ted2\">".$FDP2."/".$DP_P2;
2146 if (($DP_P2) != 0) {
2147 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2148 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2149 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2150 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2151 }
2152 else {
2153 print HTMLSNP "</td>";
2154 print TABSNP "\t";
2155 }
2156 print TABSNP "\n";
2157 print HTMLSNP "</tr>\n";
2158 }
2159 else {
2160 #
2161 print HTMLSNP "<td class=\"tedG\">".$c."</td>";
2162 print HTMLSNP "<td class=\"tedG\">".$alRef."</td>";
2163 print HTMLSNP "<td class=\"ted\">".$code_snp."</td>";
2164 print HTMLSNP "<td class=\"ted\">".$code_snp2."</td>";
2165 print HTMLSNP "<td class=\"ted\">".$FDP." / ".$DP_P;
2166 print TABSNP $s . "\t";
2167 print TABSNP $c . "\t";
2168 print TABSNP $alRef . "\t";
2169 print TABSNP $code_snp . "\t";
2170 print TABSNP $code_snp2 . "\t";
2171 print TABSNP $FDP."/".$DP_P;
2172 if (($DP_P) != 0) {
2173 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2174 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2175 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2176 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2177 }
2178 else {
2179 print HTMLSNP "</td>";
2180 print TABSNP "\t";
2181 }
2182 print TABSNP $FDP2."/".$DP_P2;
2183 print HTMLSNP "<td class=\"ted\">".$FDP2." / ".$DP_P2;
2184 if (($DP_P2) != 0) {
2185 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2186 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2187 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2188 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2189 }
2190 else {
2191 print HTMLSNP "</td>";
2192 print TABSNP "\t";
2193 }
2194 print TABSNP "\n";
2195 print HTMLSNP "</tr>\n";
2196 }
2197 $nbPolyploid1 ++ ; # SNP heterozygosity for P1
2198 $nbPolyploid2 ++ ; # SNP heterozygosity for P2
2199 $nbCommuns ++ ; # SNP heterozygosity [P1] = [P2]
2200 $taille++;
2201
2202 }
2203 else {
2204 if (($SG1 > $value_filter_p1) && ($SG2 > $value_filter_p1) && ($SG3 > $value_filter_p2) && ($SG4 > $value_filter_p2)) {
2205 if ($alAlt2 ne $alAlt) { # P1 [A/G] P2 [A/C] (3 alleles)
2206
2207
2208
2209 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2210 print HTMLSNP "<td style=\"border-left:3px solid black\">".$alRef."</td>";
2211 print HTMLSNP "<td>".$code_snp."</td>";
2212 print HTMLSNP "<td>".$code_snp2."</td>";
2213 print HTMLSNP "<td>".$FDP."/".$DP_P;
2214 print TABSNP $s . "\t";
2215 print TABSNP $c . "\t";
2216 print TABSNP $alRef . "\t";
2217 print TABSNP $code_snp . "\t";
2218 print TABSNP $code_snp2 . "\t";
2219 print TABSNP $FDP."/".$DP_P;
2220 if (($DP_P) != 0) {
2221 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2222 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2223 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2224 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2225 }
2226 else {
2227 print HTMLSNP "</td>";
2228 print TABSNP "\t";
2229 }
2230 print TABSNP $FDP2."/".$DP_P2;
2231 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2232 if (($DP_P2) != 0) {
2233 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2234 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2235 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2236 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2237 }
2238 else {
2239 print HTMLSNP "</td>";
2240 print TABSNP "\t";
2241 }
2242 print TABSNP "\n";
2243 print HTMLSNP "</tr>\n";
2244 $nbDifferent ++ ;
2245 $alleleCommunH ++ ;
2246 $taille++;
2247 }
2248 }
2249 }
2250 }
2251
2252 else { # ALL
2253 # COMMON PART
2254 #print STDOUT "\nBOUM : ".$SG1." + ".$SG2." + ".$SG3." + ".$SG4 ;
2255 #if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1) && ($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) {
2256
2257 # print HTMLSNP "<td></td><td></td>";
2258
2259 # [5] P1 = 1/1 ; P2 = 1/1 (1 allele) P1 [A] P2 [A]
2260 if (($GT_poly =~ /^1.1$/) && ($GT_poly2 =~ /^1.1$/)) {
2261
2262
2263 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2264 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2265 print HTMLSNP "<td>".$code_snp."</td>";
2266 print HTMLSNP "<td>".$code_snp2."</td>";
2267 print HTMLSNP "<td>".$FDP."/".$DP_P;
2268 print TABSNP $s . "\t";
2269 print TABSNP $c . "\t";
2270 print TABSNP $alRef . "\t";
2271 print TABSNP $code_snp . "\t";
2272 print TABSNP $code_snp2 . "\t";
2273 print TABSNP $FDP."/".$DP_P;
2274 if (($DP_P) != 0) {
2275 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2276 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2277 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2278 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2279 }
2280 else {
2281 print HTMLSNP "</td>";
2282 print TABSNP "\t";
2283 }
2284 print TABSNP $FDP2."/".$DP_P2;
2285 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2286 if (($DP_P2) != 0) {
2287 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2288 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2289 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2290 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2291 }
2292 else {
2293 print HTMLSNP "</td>";
2294 print TABSNP "\t";
2295 }
2296 print TABSNP "\n";
2297 print HTMLSNP "</tr>\n";
2298 #*********************************************************************************************************************
2299 if ($code_snp2 eq $code_snp) {
2300 $nbCommunHomo ++ ;
2301 $taille++;
2302 }
2303 else { # (2 alleles) P1 [A] P2 [C]
2304 $nbDifferent ++ ;
2305 $nbHomoDiff ++ ;
2306 $taille++;
2307 }
2308 }
2309 # [2] [4] P1 = 0/1 ; P2 = 1/1
2310 if (((($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^0.1$/)) && ($GT_poly2 =~ /^1.1$/))) {
2311 if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1)) {
2312
2313
2314
2315 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2316 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2317 print HTMLSNP "<td>".$code_snp."</td>";
2318 print HTMLSNP "<td>".$code_snp2."</td>";
2319 print HTMLSNP "<td>".$FDP."/".$DP_P;
2320 print TABSNP $s . "\t";
2321 print TABSNP $c . "\t";
2322 print TABSNP $alRef . "\t";
2323 print TABSNP $code_snp . "\t";
2324 print TABSNP $code_snp2 . "\t";
2325 print TABSNP $FDP."/".$DP_P;
2326 if (($DP_P) != 0) {
2327 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2328 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2329 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2330 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2331 }
2332 else {
2333 print HTMLSNP "</td>";
2334 print TABSNP "\t";
2335 }
2336 print TABSNP $FDP2."/".$DP_P2;
2337 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2338 if (($DP_P2) != 0) {
2339 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2340 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2341 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2342 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2343 }
2344 else {
2345 print HTMLSNP "</td>";
2346 print TABSNP "\t";
2347 }
2348 print TABSNP "\n";
2349 print HTMLSNP "</tr>\n";
2350 if ($alAlt2 ne $alAlt) { # (2 alleles) P1 [A/G] P2 [G]
2351 $nbDifferent ++ ;
2352 $alleleCommun ++ ;
2353 $nbPolyploid1 ++ ;
2354 $taille++;
2355 }
2356 else { # (3 alleles) P1 [A/G] P2 [C]
2357 $nbDifferent ++ ;
2358 $alleleDifferent ++ ;
2359 $nbPolyploid1 ++ ;
2360 $taille++;
2361 }
2362 }
2363 }
2364 if ((($GT_poly2 =~ /^0.1$/) || ($GT_poly2 =~ /^0.1$/)) && ($GT_poly =~ /^1.1$/)) {
2365 if (($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) {
2366 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2367 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2368 print HTMLSNP "<td>".$code_snp."</td>";
2369 print HTMLSNP "<td>".$code_snp2."</td>";
2370 print HTMLSNP "<td>".$FDP."/".$DP_P;
2371 print TABSNP $s . "\t";
2372 print TABSNP $c . "\t";
2373 print TABSNP $alRef . "\t";
2374 print TABSNP $code_snp . "\t";
2375 print TABSNP $code_snp2 . "\t";
2376 print TABSNP $FDP."/".$DP_P;
2377 if (($DP_P) != 0) {
2378 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2379 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2380 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2381 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2382 }
2383 else {
2384 print HTMLSNP "</td>";
2385 print TABSNP "\t";
2386 }
2387 print TABSNP $FDP2."/".$DP_P2;
2388 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2389 if (($DP_P2) != 0) {
2390 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2391 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2392 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2393 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2394 }
2395 else {
2396 print HTMLSNP "</td>";
2397 print TABSNP "\t";
2398 }
2399 print TABSNP "\n";
2400 print HTMLSNP "</tr>\n";
2401 if ($alAlt2 ne $alAlt) { # (2 alleles) P1 [A/G] P2 [G]
2402 $nbDifferent ++ ;
2403 $alleleCommun ++ ;
2404 $nbPolyploid2 ++ ;
2405 $taille++;
2406 }
2407 else { # (3 alleles) P1 [A/G] P2 [C]
2408 $nbDifferent ++ ;
2409 $alleleDifferent ++ ;
2410 $nbPolyploid2 ++ ;
2411 $taille++;
2412 }
2413 }
2414 }
2415 # [3] [7] P1 = 0/1 ; P2 = 0/0 (2 alleles) P1 [A/G] P2 [A]
2416 if ((($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^0.1$/)) && (($GT_poly2 =~ /^0.0$/) || ($GT_poly2 eq ""))) {
2417 if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1)) {
2418 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2419 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2420 print HTMLSNP "<td>".$code_snp."</td>";
2421 print HTMLSNP "<td>".$code_snp2."</td>";
2422 print HTMLSNP "<td>".$FDP."/".$DP_P;
2423 print TABSNP $s . "\t";
2424 print TABSNP $c . "\t";
2425 print TABSNP $alRef . "\t";
2426 print TABSNP $code_snp . "\t";
2427 print TABSNP $code_snp2 . "\t";
2428 print TABSNP $FDP."/".$DP_P;
2429 if (($DP_P) != 0) {
2430 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2431 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2432 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2433 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2434 }
2435 else {
2436 print HTMLSNP "</td>";
2437 print TABSNP "\t";
2438 }
2439 print TABSNP $FDP2."/".$DP_P2;
2440 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2441 if (($DP_P2) != 0) {
2442 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2443 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2444 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2445 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2446 }
2447 else {
2448 print HTMLSNP "</td>";
2449 print TABSNP "\t";
2450 }
2451 print TABSNP "\n";
2452 print HTMLSNP "</tr>\n";
2453
2454 $nbDifferent ++ ;
2455 $alleleCommun ++ ;
2456 $nbPolyploid1 ++ ;
2457 $taille++;
2458 }
2459 }
2460 if ((($GT_poly2 =~ /^0.1$/) || ($GT_poly2 =~ /^0.1$/)) && (($GT_poly =~ /^0.0$/) || ($GT_poly eq ""))) {
2461 if (($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) {
2462 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2463 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2464 print HTMLSNP "<td>".$code_snp."</td>";
2465 print HTMLSNP "<td>".$code_snp2."</td>";
2466 print HTMLSNP "<td>".$FDP."/".$DP_P;
2467 print TABSNP $s . "\t";
2468 print TABSNP $c . "\t";
2469 print TABSNP $alRef . "\t";
2470 print TABSNP $code_snp . "\t";
2471 print TABSNP $code_snp2 . "\t";
2472 print TABSNP $FDP."/".$DP_P;
2473 if (($DP_P) != 0) {
2474 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2475 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2476 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2477 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2478 }
2479 else {
2480 print HTMLSNP "</td>";
2481 print TABSNP "\t";
2482 }
2483 print TABSNP $FDP2."/".$DP_P2;
2484 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2485 if (($DP_P2) != 0) {
2486 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2487 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2488 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2489 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2490 }
2491 else {
2492 print HTMLSNP "</td>";
2493 print TABSNP "\t";
2494 }
2495 print TABSNP "\n";
2496 print HTMLSNP "</tr>\n";
2497 ############
2498 # HERE P2 #
2499 ############
2500 $nbDifferent ++ ;
2501 $alleleCommun ++ ;
2502 $nbPolyploid2 ++ ;
2503 $taille++;
2504 }
2505 }
2506 # [6] [8] P1 = 1/1 ; P2 = 0/0
2507 if (($GT_poly =~ /^1.1$/) && (($GT_poly2 =~ /^0.0$/) || ($GT_poly2 eq ""))) {
2508 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2509 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2510 print HTMLSNP "<td>".$code_snp."</td>";
2511 print HTMLSNP "<td>".$code_snp2."</td>";
2512 print HTMLSNP "<td>".$FDP."/".$DP_P;
2513 print TABSNP $s . "\t";
2514 print TABSNP $c . "\t";
2515 print TABSNP $alRef . "\t";
2516 print TABSNP $code_snp . "\t";
2517 print TABSNP $code_snp2 . "\t";
2518 print TABSNP $FDP."/".$DP_P;
2519 if (($DP_P) != 0) {
2520 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2521 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2522 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2523 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2524 }
2525 else {
2526 print HTMLSNP "</td>";
2527 print TABSNP "\t";
2528 }
2529 print TABSNP $FDP2."/".$DP_P2;
2530 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2531 if (($DP_P2) != 0) {
2532 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2533 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2534 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2535 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2536 }
2537 else {
2538 print HTMLSNP "</td>";
2539 print TABSNP "\t";
2540 }
2541 print TABSNP "\n";
2542 print HTMLSNP "</tr>\n";
2543 $nbDifferent ++ ;
2544 $alleleCommun ++ ;
2545 $nbPolyploid1 ++ ;
2546 $taille++;
2547 }
2548 if (($GT_poly2 =~ /^1.1$/) && (($GT_poly =~ /^0.0$/) || ($GT_poly eq ""))) {
2549 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
2550 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
2551 print HTMLSNP "<td>".$code_snp."</td>";
2552 print HTMLSNP "<td>".$code_snp2."</td>";
2553 print HTMLSNP "<td>".$FDP."/".$DP_P;
2554 print TABSNP $s . "\t";
2555 print TABSNP $c . "\t";
2556 print TABSNP $alRef . "\t";
2557 print TABSNP $code_snp . "\t";
2558 print TABSNP $code_snp2 . "\t";
2559 print TABSNP $FDP."/".$DP_P;
2560 if (($DP_P) != 0) {
2561 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
2562 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
2563 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
2564 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
2565 }
2566 else {
2567 print HTMLSNP "</td>";
2568 print TABSNP "\t";
2569 }
2570 print TABSNP $FDP2."/".$DP_P2;
2571 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
2572 if (($DP_P2) != 0) {
2573 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
2574 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
2575 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
2576 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
2577 }
2578 else {
2579 print HTMLSNP "</td>";
2580 print TABSNP "\t";
2581 }
2582 print TABSNP "\n";
2583 print HTMLSNP "</tr>\n";
2584 $nbDifferent ++ ;
2585 $alleleCommun ++ ;
2586 $nbPolyploid2 ++ ;
2587 $taille++;
2588 }
2589 #}
2590 }
2591
2592
2593 #print TABSNP $s."\t".$c."\t".$alRef."\t".$code_snp."\t".$code_snp2."\t".$FDP."\t".$DP_P."\t".$FDP2."\t".$DP_P2;
2594
2595 $ligneOK = 1 ;
2596 }
2597
2598
2599 if (($nbCommuns + $nbCommunHomo + $nbDifferent + $nbHomoDiff + $alleleCommun + $alleleDifferent + $alleleCommunH + $nbPolyploid1 + $nbPolyploid2) > 0 ) {
2600
2601 if ($ligneInter == 0) {
2602 print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">".$s."</td>";
2603 }
2604 else {
2605 print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">".$s."</td>";
2606 }
2607 print TABCOUNT $s."\t";
2608
2609 #######################################
2610 if ($ligneInter == 0) { $ligneInter = 1 ; }
2611 else { $ligneInter = 0 ; }
2612 #######################################
2613
2614 # Calcul des intervalles #
2615 ##########################
2616 $taille_totale = 0 ;
2617 my $ref = $intervalle2{$s};
2618 my %hash = %$ref;
2619
2620 foreach my $interval(keys(%hash)){
2621 my @pos = split(/-/,$interval);
2622 $taille_inter = $pos[1]-$pos[0]+1 ;
2623 $taille_totale = $taille_totale + $taille_inter;
2624 }
2625 $total1 = $case5 + $case1 + $case2 + $casePolyplother;
2626 $total2 = $case5 + $case3ou4 + $caseDiplother;
2627
2628 # SYNTHESIS
2629
2630 print HTMLCOUNT "<td>".$taille_totale."</td><td style=\"border-left:3px solid black\">".$taille. "</td></td>";
2631 print HTMLCOUNT "<td style=\"border-left:3px solid black\">";
2632 print HTMLCOUNT $nbCommuns."</td><td>".$nbCommunHomo."</td><td style=\"border-left:3px solid black\">".$nbDifferent."</td><td style=\"border-left:3px solid black\">";
2633 print HTMLCOUNT $nbHomoDiff."</td><td>".$alleleCommun."</td><td>".$alleleDifferent."</td><td>".$alleleCommunH."</td>";
2634 print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$nbPolyploid1."</td><td>".$nbPolyploid2."</td>";
2635 print TABCOUNT $taille_totale."\t".$taille."\t";
2636 print TABCOUNT $nbCommuns."\t".$nbCommunHomo."\t".$nbDifferent."\t".$nbHomoDiff."\t".$alleleCommun."\t".$alleleDifferent."\t".$alleleCommunH."\t".$nbPolyploid1."\t".$nbPolyploid2."\t";
2637
2638 $nbTotGenesAna ++ ;
2639
2640 print HTMLCOUNT "</tr>";
2641 print TABCOUNT "\n";
2642
2643 $totalSize = $totalSize + $taille_totale ;
2644 $totalSNP = $totalSNP + $taille ;
2645 $totalNbPolyploid1 = $totalNbPolyploid1 + $nbPolyploid1 ; # SNP heterozygosity for P1
2646 $totalNbPolyploid2 = $totalNbPolyploid2 + $nbPolyploid2 ; # SNP heterozygosity for P2
2647 $totalNbCommuns = $totalNbCommuns + $nbCommuns ; # SNP heterozygosity [P1] = [P2]
2648 $totalNbCommunsHomo = $totalNbCommunsHomo + $nbCommunHomo ; # SNP homozygosity [P1] = [P2]
2649 $totalNbDifferent = $totalNbDifferent + $nbDifferent ; # [P1] ne [P2]
2650 $totalNbAlleleCommun = $totalNbAlleleCommun + $alleleCommun ; # Example : P1 = [A/G] ; P2 = [A]
2651 $totalAlleleDifferent = $totalAlleleDifferent + $alleleDifferent ; # Example : P1 = [A/G] ; P2 = [C] or [T]
2652 $totalAlleleCommunH = $totalAlleleCommunH + $alleleCommunH ; # Example : P1 = [A/G] ; P2 = [A/C]
2653 $totalNbHomoDiff = $totalNbHomoDiff + $nbHomoDiff ; # Example : P1 = [A/G] ; P2 = [A/C]
2654 }
2655
2656
2657
2658
2659 }
2660 ########## MODIF DERNIERE MINUTE ################"
2661 print HTMLCOUNT "<tr class=\"td3\">\n<td>";
2662
2663 print HTMLCOUNT $nbTotGenesAna."<td style=\"border-left:3px solid black\">";
2664 print HTMLCOUNT $totalSize."</td><td style=\"border-left:3px solid black\">";
2665 print HTMLCOUNT $totalSNP."</td><td style=\"border-left:3px solid black\">";
2666 print HTMLCOUNT $totalNbCommuns."</td><td>";
2667 print HTMLCOUNT $totalNbCommunsHomo."</td><td>";
2668 print HTMLCOUNT $totalNbDifferent."</td><td style=\"border-left:3px solid black\">";
2669 print HTMLCOUNT $totalNbHomoDiff."</td><td style=\"border-left:3px solid black\">";
2670 print HTMLCOUNT $totalNbAlleleCommun."</td><td style=\"border:3px solid black\">";
2671 print HTMLCOUNT $totalAlleleDifferent."</td><td style=\"border:3px solid black\">";
2672 print HTMLCOUNT $totalAlleleCommunH."</td><td>";
2673 print HTMLCOUNT $totalNbPolyploid1."</td><td>";
2674 print HTMLCOUNT $totalNbPolyploid2."</td>";
2675 print HTMLCOUNT "</tr>";
2676
2677
2678 print TABCOUNT "$nbTotGenesAna\t$totalSize\t$totalSNP\t$totalNbCommuns\t$totalNbCommunsHomo\t$totalNbDifferent\t$totalNbHomoDiff\t$totalNbAlleleCommun\t$totalAlleleDifferent\t$totalAlleleCommunH\t$totalNbPolyploid1\t$totalNbPolyploid2\t";
2679 print TABCOUNT "\n";
2680
2681 ####################################################
2682 print HTMLSNP "</table>\n";
2683 print HTMLSNP "</html>\n";
2684 close HTMLSNP ;
2685
2686 print HTMLCOUNT "</table>\n";
2687 print HTMLCOUNT "</html>\n";
2688 close HTMLCOUNT ;
2689
2690 close TABSNP;
2691 close TABCOUNT ;
2692
2693 # tie @array, 'Tie::File', $SNP_count or die ;
2694 # $array[82] = "<table class=\"tab2\"><th class=\"th\" style=\"text-align:left;\">";
2695 # $array[83] = "<br>".$nbTotGenesAna." analysed genes";
2696 # $array[84] = "<br>".$nbTotGenesVal." with SNP validation";
2697 # $array[85] = "<br>Analysis performed on ".$totalSize." bp";
2698 # $array[86] = "<br>".$totalSNP." SNP";
2699 # $array[87] = "<br><img src=\"".$REPimages."5v.png\" WIDTH=20> : ".$total5." validated SNP";
2700 # $array[88] = "<br><br><img src=\"".$REPimages."1.png\" WIDTH=20> : ".$total11."";
2701 # $array[89] = "<br><img src=\"".$REPimages."2.png\" WIDTH=20> : ".$total22."";
2702 # $array[90] = "<br><img src=\"".$REPimages."3ou4.png\" WIDTH=20> : ".$total3ou4."";
2703 # $array[91] = "<br>Other SNP types : ".$totalOther."";
2704 # $array[92] = "<br>Heterozygosity for genome 1 : ".$totalGenome2."";
2705 # $array[93] = "<br>SNP between parental genomes (diploids) : ".$total512."";
2706 # $array[94] = "<br>SNP polyploid : ".$total534."";
2707 # $array[95] = "<th class=\"th\"><img src=\"".$REPimages."arbre.png\" WIDTH=400></th></table>";
2708 }
2709
2710 $time2 = time ;
2711 $tmps = $time2 - $time;
2712 print STDOUT "\n\nTemps execution : ".$tmps."\n";