Mercurial > repos > dereeper > sniploid2
view SNiPloid.pl @ 0:e94de0ea3351 draft default tip
Uploaded
| author | dereeper |
|---|---|
| date | Wed, 11 Sep 2013 09:08:15 -0400 |
| parents | |
| children |
line wrap: on
line source
#!/usr/bin/perl use Getopt::Long; use Switch; use Tie::File; ##################################################### # # # @@@@ @ @ @ @@@@ @ @ @ # # @ @@ @ @ @ @ @ # # @@@ @ @ @ @ @@@@ @ @@@ @ @@@@ # # @ @ @@ @ @ @ @ @ @ @ @ # # @@@@ @ @ @ @ @ @@@ @ @@@ # # # ##################################################### ############################################################################################################### # # SNiPloid # Author : Marine PERALTA # ############################################################################################################### # # Galaxy Version # ############################################################################################################### #___________________________________ # Samples names #----------------------------------- $polyploidName = "" ; $polyploid2Name = "" ; # $genome1Name = "" ; $genome2Name = "" ; #___________________________________ # VCF files #----------------------------------- $VCFpolyploid = "" ; $VCFpolyploid2 = "" ; # $VCFgenome1 = "" ; $VCFgenome2 = "" ; $merged_VCF = "" ; # Polyploid + Genome1 + Genome 2 #___________________________________ # Depth of Coverage File #----------------------------------- $DOCpolyploid = "" ; $DOCpolyploid2 = "" ; # $DOCgenome1 = "" ; $DOCgenome2 = "" ; $merged_DOC = "" ; # Polyploid + Genome1 + Genome 2 #___________________________________ # Depth for each sample #----------------------------------- $depthPolyploid = 0 ; $depthPolyploid2 = 0 ; # $depthGenome1 = 0 ; $depthGenome2 = 0 ; #___________________________________ # Output Files #----------------------------------- $SNP_csv = "SNP_tab.txt"; $SNP_html = "SNP_view.html"; $SNP_count = "SNP_synthesis_tab.html"; $SNP_count_csv = "SNP_synthesis_tab.txt"; #___________________________________ # Other parameters #----------------------------------- $enableLowQuality = 0 ; #default value for enable quality SNP = only PASS SNP are considered $ref = 0 ; # default parameter = extern $filtre_ouPas = 0 ; $value_filter_p1 = 0 ; $value_filter_p2 = 0 ; $REPimages = "img_sniploid/"; $poly_poly_analysis = 0 ; my $usage = qq~ Basic usage For comparison between a polyploid and its parental diploid genomes: $0 --vp <VCF_polyploid> --vg1 <VCF_diploid> --cpp <depth_polyploid> --cg1 <depth_diploid> --dp <min_depth_polyploid> --dg1 <min_depth_diploid> --ref 1 For comparison between 2 polyploids: $0 --vp <VCF_polyploid1> --vp2 <VCF_polyploid2> --cpp <depth_polyploid1> --cpp2 <depth_polyploid2> --dp <min_depth_polyploid1> --dp2 <min_depth_polyploid2> Usage:$0 <args> where <args> are: --vp <VCF file for polyploid> --vp2 <VCF file for polyploid 2> --vg1 <VCF file for diploid genome 1> --vg2 <VCF file for diploid genome 2> --cpp <Depth file for polyploid> --cpp2 <Depth file for polyploid 2> --cg1 <Depth file for diploid genome 1> --cg2 <Depth file for diploid genome 2> --dp <Minimum read depth at a position to make a call for polyploid> --dp2 <Minimum read depth at a position to make a call for polyploid 2> --dg1 <Minimum read depth at a position to make a call for diploid genome 1> --dg2 <Minimum read depth at a position to make a call for diploid genome 2> --oc <Output file name for SNP list in csv> --oh <Output file name for SNP list in HTML> --ocs <Output file name for SNP count per gene in csv> --ohs <Output file name for SNP count per gene in HTML> --vfp1 <Minimul allele frequency to consider as variant for polyploid 1 (in %). Default: 0> --vfp2 <Minimul allele frequency to consider as variant for polyploid 2 (in %). Default: 0> --elq <Enable low quality SNP tag. Default: 0> --gn2 <Specify a name for diploid genome 2> --ref <The reference must be included in the analysis as diploid genome. Default: 0> ~; $usage .= "\n"; =pod Add option for "Heterozygosity" Enable "heterozygosity" for genome 1 (reference intern) - not necessary... Enable "heterozygosity" for genome 1 and genome 2 (reference extern) =cut GetOptions ( # "pn=s" => \$polyploidName, # "pn2=s" => \$polyploid2Name, # # "gn1=s" => \$genome1Name, "gn2=s" => \$genome2Name, "vp=s" => \$VCFpolyploid, "vp2=s" => \$VCFpolyploid2, # "vg1=s" => \$VCFgenome1, "vg2=s" => \$VCFgenome2, "vm=s" => \$merged_VCF, "cpp=s" => \$DOCpolyploid, "cpp2=s" => \$DOCpolyploid2, # "cg1=s" => \$DOCgenome1, "cg2=s" => \$DOCgenome2, "cm=s" => \$merged_DOC, "dp=i" => \$depthPolyploid, "dp2=i" => \$depthPolyploid2, # "dg1=i" => \$depthGenome1, "dg2=i" => \$depthGenome2, "oc=s" => \$SNP_csv, "oh=s" => \$SNP_html, "ohs=s" => \$SNP_count, "ocs=s" => \$SNP_count_csv, "elq=i" => \$enableLowQuality, "ref=i" => \$ref, #"fop=i" => \$filtre_ouPas, "vfp1=i" => \$value_filter_p1, "vfp2=i" => \$value_filter_p2, "img=s" => \$REPimages # h = i = > \ $heterozygosity , ); # Validation - Samples names die $usage if ( (!$VCFgenome1 || !$DOCgenome1 ) && (!$VCFpolyploid || !$DOCpolyploid) || (!$VCFpolyploid2 || !$DOCpolyploid2 ) && (!$VCFpolyploid || !$DOCpolyploid)); %intervalle1 ; %intervalle2 ; %snp = () ; my %snp_final ; my %five = () ; my %phased_regions = () ; $nbTotGenes = 0 ; $nbTotGenesVal = 0 ; $nbTotGenesAna = 0 ; if ($VCFpolyploid2 ne "") { $poly_poly_analysis = 1 ; } # if ($polyploidName eq "") { # print STDOUT "*** /!\\ ERROR: Missing name for polyploid - You have to specify a name for the polyploid species [--pn \"polyploid_name\"] $!" ; # die ("*** /!\\ ERROR: Missing name for polyploid - You have to specify a name for the polyploid species [--pn \"polyploid_name\"] $!") ; # } if ($poly_poly_analysis == 1) { print STDOUT "\nAnalysis Type: Polyploid vs Polyploid\n---------------------------------------"; # print STDOUT "\nPolyploid 1: ".$polyploidName ; # print STDOUT "\nPolyploid 2:".$polyploid2Name ; # if ($polyploid2Name eq "") { # print STDOUT "*** /!\\ ERROR: Missing name for polyploid 2 - You have to specify a name for the polyploid species 2 [--pn2 \"polyploid_2_name\"] $!" ; # die ("*** /!\\ ERROR: Missing name for polyploid - You have to specify a name for the polyploid species 2 [--pn \"polyploid_2_name\"] $!") ; # } } else { print STDOUT "\nAnalysis Type: Polyploid vs Parental Genomes\n---------------------------------------"; # print STDOUT "\nPolyploid: ".$polyploidName ; # print STDOUT "\nGenome 1: ".$genome1Name ; # print STDOUT "\nGenome 2: ".$genome2Name ; # if ($genome1Name eq "") { # die ("*** /!\\ ERROR: Missing name for genome 1 - You have to specify a name for the genome 1 species") ; # } # if ($genome2Name eq "") { # die ("*** /!\\ ERROR: Missing name for genome 2 - You have to specify a name for the genome 2 species") ; # } # Validation - depth if ($depthPolyploid == 0) { die ("*** /!\\ ERROR: Missing depth information for polyploid"); } if ($depthGenome1 == 0) { die ("*** /!\\ ERROR: Missing depth information for genome 1"); } if ($ref == 0 && $depthGenome2 == 0) { die ("*** /!\\ ERROR: Missing depth information for genome 2"); } } $time = time ; ################################################################ # 1) Polyploid vs Polyploid analysis ################################################################ if ($poly_poly_analysis == 1) { #print STDOUT "\n PASS"; &Intervall_part1($DOCpolyploid) ; &Intervall_part2($DOCpolyploid2,$depthPolyploid2) ; &VCF_Analysis($VCFpolyploid); &VCF_Analysis($VCFpolyploid2); # CSS, titles, img, etc. &intro_output ; &poly_poly_output ; } ################################################################ # 2) Polyploid vs Parental Diploid Genomes Analysis ################################################################ else { # PART 1 : CREATING COMMON INTERVALS &Intervall_part1($DOCpolyploid) ; &Intervall_part2($DOCgenome1,$depthGenome1) ; if ($ref == 0) { # genome2 => no parental genome as reference &Intervall_part2($DOCgenome2,$depthGenome2) ; } # PART 2 and 3 : CREATING SNP TAB AND OUTPUTS # VCF_Analysis : Create SNP hash and phasing &VCF_Analysis($VCFpolyploid); if ($ref == 1) { # Reference = one of two parental genomes &VCF_Analysis($VCFgenome1); # CSS, titles, img, etc. &intro_output ; # SNP Comparison and display &int_output ; } else { # Extern Reference &VCF_Analysis($VCFgenome1); &VCF_Analysis($VCFgenome2); # CSS, titles, img, etc. &intro_output ; # SNP Comparison and display &ext_output ; } } sub Intervall_part1 { my(@args) = @_; #print STDOUT "\nTEST ::: ".$args[0] ; open (TABSNP, $args[0]) or die ("Pbm a l'ouverture du fichier : $args[0]"); @DOC = <TABSNP> ; close TABSNP ; $rec = 0 ; $position_pre ; $val_deb = ""; $val_fin = ""; $name_pre = ""; foreach $line(@DOC) { if ($line ne $DOC[0]) { @ligne = split(/\t/ , $line); @position = split(/:/ , $ligne[0]); $name_gene = $position[0] ; if ($merged == 0) { # 1st File - Polyploid $depthcov = $ligne[1] ; if ($name_gene){ if ($name_gene ne $gene_pre) { if ($rec == 1) { $position_fin = $position_pre ; $val_fin = $val_deb.$position_fin ; # Intervalle end position $intervalle1{$gene_pre}{$val_fin} = "ok" ; } $rec = 0; } if ($depthcov >= $depthPolyploid){ if ($rec == 0) { $position_deb = $position[1] ; $val_deb = $position_deb."-"; # Intervalle start position } $rec = 1 ; } if ($depthcov < $depthPolyploid){ if ($rec == 1) { $position_fin = $position_pre ; $val_fin = $val_deb.$position_fin ; # Intervalle end position $intervalle1{$gene_pre}{$val_fin} = "ok" ; } $rec = 0; } } } else { # Merged files (2 or 3 species) if ($ref == 0) { # 3 species $depthcov1 = $ligne[$indiceGenome2] ; $depthcov2 = $ligne[$indicePolyploid1] ; $depthcov3 = $ligne[$indiceGenome1] ; if ($name_gene){ if (($depthcov1 >= $depthGenome2) && ($depthcov2 >= $depthPolyploid)&& ($depthcov3 >= $depthGenome1)){ if ($rec == 0) { $position_deb = $position[1] ; $val_deb = $position_deb."-"; } $rec = 1 ; } if (($depthcov1 < $depthGenome2) || ($depthcov2 < $depthPolyploid) || ($depthcov3 < $depthGenome1)){ if ($rec == 1) { $position_fin = $position_pre ; $val_fin = $val_deb.$position_fin ; $intervalle1{$gene_pre}{$val_fin} = "ok" ; } $rec = 0 ; } } } else { # 2 species $depthcov1 = $ligne[$indicePolyploid1] ; $depthcov2 = $ligne[$indiceGenome1] ; if ($name_gene){ if (($depthcov1 >= $depthPolyploid) && ($depthcov2 >= $depthGenome1)){ if ($rec == 0) { $position_deb = $position[1] ; $val_deb = $position_deb."-"; } $rec = 1 ; } if (($depthcov1 < $depthPolyploid) || ($depthcov2 < $depthGenome1)){ if ($rec == 1) { $position_fin = $position_pre ; $val_fin = $val_deb.$position_fin ; $intervalle1{$gene_pre}{$val_fin} = "ok" ; } $rec = 0 ; } } } } $position_pre = $position[1] ; $gene_pre = $name_gene ; } } return (%intervalle1) ; } sub Intervall_part2 { my(@args) = @_; #print "\nintervall part 2 : $args[1]"; open (TABSNP, $args[0]) or die ("Pbm a l'ouverture du fichier : $args[0]"); #print STDOUT "\n$args[0]"; @DOC = <TABSNP> ; my %tab ; foreach $li(@DOC) { if ($li =~ /^(.+):(.+)\t(.+)\t.+\t.+$/) { $tab{$1}{$2} = $3; } } close TABSNP ; $rec = 0 ; $position_pre ; $val_deb = ""; $val_fin = ""; foreach my $interval(sort (keys(%intervalle1))){ my $ref = $intervalle1{$interval}; my %intervalls = %$ref; $name_gene = $interval ; foreach my $intervall(sort (keys(%intervalls))){ $final = 2 ; $rec = 0 ; ($debut,$fin) = split(/-/,$intervall); for ($i=$debut; $i <=$fin; $i++) { if ($tab{$interval}{$i} >= $args[1]){ if ($rec == 0) { $position_deb = $i ; $val_deb = $position_deb."-"; } $rec = 1 ; $final = 0 ; } if ($tab{$interval}{$i} < $args[1]){ $final = 1 ; if ($rec == 1) { $position_fin = $i-1 ; $val_fin = $val_deb.$position_fin ; $intervalle2{$name_gene}{$val_fin} = "ok" ; } $rec = 0 ; } } if ($final == 0) { $val_fin = $val_deb.$fin ; $intervalle2{$name_gene}{$val_fin} = "ok" ; } } } if ($VCFgenome2 ne ""){ %intervalle1 = %intervalle2 ; } foreach my $interval(sort (keys(%intervalle2))){ my $ref = $intervalle2{$interval}; my %intervalls = %$ref; $name_gene = $interval ; } return (%intervalle2) ; } sub VCF_Analysis { %snp_final = () ; $compt_phasing = 0 ; $compt_five = 0 ; my(@args) = @_; open (TABSNP, "$args[0]") or die ("ERROR : file $args[0] don't exists"); @VCF = <TABSNP> ; close TABSNP ; ########################################### # test if VCF was filtered ########################################### my $vcf_file = $args[0]; my $grep_pass = `grep -c 'PASS' $vcf_file`; chomp($grep_pass); my $pass = "PASS"; if (defined $grep_pass && $grep_pass == 0) { $pass = "."; } #print "$pass $grep_pass $vcf_file\n"; foreach $line(@VCF){ if ($line =~ /^#CHROM.+FORMAT\t(.+)$/) { $name_record = $1 ; } if ($line !~ /^#/){ @infos_line = split(/\t/,$line) ; $gene = $infos_line[0]; $position = $infos_line[1]; $ref_allele = $infos_line[3]; $alt_allele = $infos_line[4]; if ($ref_allele =~/\w\w/ or $alt_allele =~/\w\w/) { next; } $snp_code = "[$ref_allele/$alt_allele]"; $quality_of_snp = $infos_line[6]; $depth_recuperation = $infos_line[7]; $alleles = $infos_line[9]; ($GT,$AD,$FDP,$GQ,$PL) = split(":",$alleles); # PHASING if (($GT =~ /\|/) && ($previous_GT =~ /\//)) { # initialisation région $compt_phasing ++ ; $phased_regions{$gene}{$compt_phasing}{$previous_position} = $previous_GT ; $phased_regions{$gene}{$compt_phasing}{$position} = $GT ; } if (($GT =~ /\|/) && ($previous_GT =~ /\|/)) { # extension région $phased_regions{$gene}{$compt_phasing}{$position} = $GT ; } # $FDP = Filtered Depth # $DP = Total Depth my $DP; my @tags = split(";",$depth_recuperation); foreach my $tag(@tags) { if ($tag =~/DP=/) { $DP = $tag; } } #($sub1,$sub2) = split(",",$AD); #$somme = $sub1 + $sub2 ; $somme = 0; my @depth_of_alleles = split(",",$AD); my $sub1 = $depth_of_alleles[0]; foreach my $depth_of_allele(@depth_of_alleles) { $somme += $depth_of_allele; } if ($somme == 0 ) { print STDOUT "ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\""; die ("ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\""); } else { $ratio = ($sub1/$somme)*100; $ratio = sprintf("%.0f", $ratio); } @DP = split ("=",$DP) ; $test_inside_interval = 0 ; my $ref = $intervalle2{$gene}; my %hash = %$ref; foreach my $interval(keys(%hash)){ my @pos = split(/-/,$interval) ; if ($position >= $pos[0] && $position <= $pos[1]) { $test_inside_interval = 1 ; last ; } } # ENABLE LOW_QUALITY SNP if ($enableLowQuality == 1) { if ($test_inside_interval == 1 ){ # if ($args[0] eq $VCFpolyploid) { # Polyploid $polyploidName = $name_record ; $snp{$gene}{$position} = $snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ; } else { if ($args[0] eq $VCFgenome1) { # genome1 $genome1Name = $name_record ; if (exists $snp{$gene}{$position}) { # if polyploid SNP $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT ; ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp{$gene}{$position}); @recupAlleles = split(/\[/,$code_snp); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAltP) = split(/\//,$recupAlleles[0]); @recupAlleles = split(/\[/,$code_G1); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$code_G1) = split(/\//,$recupAlleles[0]); #print "\nINFOS\n".$GT_poly."\t"; #print $GT_G1."\t"; #print $code_G1."\t"; #print $alAltP."\n"; if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) { $five{$gene}{$position} = $GT_poly ; } } else { # if no polyploid SNP, key is empty $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$GT ; } } else { # genome2 if ($args[0] eq $VCFgenome2) { $genome2Name = $name_record ; if (exists $snp{$gene}{$position}) { # if polyploid SNP $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT; } else { # if no polyploid SNP and no genome1, key is empty $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$ref_allele."\t\t".$snp_code."\t".$GT ; } } } if ($args[0] eq $VCFpolyploid2) { # polyploid2 $polyploid2Name = $name_record ; if (exists $snp{$gene}{$position}) { # if polyploid SNP $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ; } else { # if no polyploid SNP, key is empty $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ; } } } } } # ONLY PASS SNP CONSIDERED else { if (($test_inside_interval == 1 ) && ($quality_of_snp eq $pass) && ($snp{$gene}{$position} ne "LQ")){ # if ($args[0] eq $VCFpolyploid) { # Polyploid $polyploidName = $name_record ; $snp{$gene}{$position} = $snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ; } else { if ($args[0] eq $VCFgenome1) { # genome1 $genome1Name = $name_record ; if (exists $snp{$gene}{$position}) { # if polyploid SNP $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT ; ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp{$gene}{$position}); @recupAlleles = split(/\[/,$code_snp); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAltP) = split(/\//,$recupAlleles[0]); @recupAlleles = split(/\[/,$code_G1); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$code_G1) = split(/\//,$recupAlleles[0]); #print "\nINFOS\n".$GT_poly."\t"; #print $GT_G1."\t"; #print $code_G1."\t"; #print $alAltP."\n"; if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) { $five{$gene}{$position} = $GT_poly ; } } else { # if no polyploid SNP, key is empty $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$GT ; } } else { # genome2 if ($args[0] eq $VCFgenome2) { $genome2Name = $name_record ; if (exists $snp{$gene}{$position}) { # if polyploid SNP $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT; } else { # if no polyploid SNP and no genome1, key is empty $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$ref_allele."\t\t".$snp_code."\t".$GT ; } } } if ($args[0] eq $VCFpolyploid2) { # polyploid2 $polyploid2Name = $name_record ; if (exists $snp{$gene}{$position}) { # if polyploid SNP $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ; } else { # if no polyploid SNP, key is empty $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ; } } } } else { if ($quality_of_snp ne $pass) { $snp{$gene}{$position} = "LQ"; } } } ################################################################################################################################ } $previous_GT = $GT ; $previous_position = $position ; } foreach my $s(sort(keys(%snp))){ my $ref = $snp{$s}; my %hash = %$ref; foreach my $snip(keys(%hash)){ if ($snp{$s}{$snip} ne "LQ"){ $snp_final{$s}{$snip} = $snp{$s}{$snip} ; } } } return (%snp_final) ; } sub intro_output { ########################################################### # ANALYSE - CREATION FICHIERS DE SORTIE # ########################################################### # Ouverture des fichiers open (HTMLSNP, ">$SNP_html"); open (TABSNP, ">$SNP_csv"); open (HTMLCOUNT, ">$SNP_count"); open (TABCOUNT, ">$SNP_count_csv"); print HMTL "<html>\n"; print HTMLCOUNT "<html>\n"; print HTMLSNP "<head>\n"; print HTMLCOUNT "<head>\n"; ##################################################### # CSS # ##################################################### print HTMLSNP "<style type=\"text/css\">\n"; print HTMLSNP "th {\n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " border-width:3px;\n"; print HTMLSNP " font-family: calibri;\n"; print HTMLSNP " }\n"; print HTMLSNP "body {text-align:center;}\n"; print HTMLSNP "table {\n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " margin:auto;\n"; print HTMLSNP " border-collapse: collapse;\n"; print HTMLSNP " border-width:3px; \n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " }\n"; print HTMLSNP ".bord1 { \n"; print HTMLSNP " font-size: 11pt;\n"; print HTMLSNP " font-family: calibri;\n"; print HTMLSNP " border-width:1px;\n"; print HTMLSNP " border-top:3px;\n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-right:3px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " background-color : #c6c3bd; \n"; print HTMLSNP " }\n"; print HTMLSNP ".bord2 { \n"; print HTMLSNP " font-size: 11pt;\n"; print HTMLSNP " font-family: calibri;\n"; print HTMLSNP " border-width:1px;\n"; print HTMLSNP " border-top:3px;\n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-right:3px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " background-color : #c6c3ee; \n"; print HTMLSNP " }\n"; print HTMLSNP "td { \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " }\n"; print HTMLSNP ".tdm { \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " }\n"; print HTMLSNP ".td1 { \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " font-size: 11pt;\n"; print HTMLSNP " font-family: calibri;\n"; print HTMLSNP " border-width:1px;\n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-right:3px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " background-color : #c6c3bd; \n"; print HTMLSNP " }\n"; print HTMLSNP ".td2 { \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " font-size: 11pt;\n"; print HTMLSNP " font-family: calibri;\n"; print HTMLSNP " border-width:1px;\n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-right:3px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " background-color : #c6c3ee; \n"; print HTMLSNP " }\n"; print HTMLSNP ".ted { \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " font-weight : bold;\n"; print HTMLSNP " background-color : #A19EED; \n"; print HTMLSNP " }\n"; print HTMLSNP ".ted2 { \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " font-weight : bold;\n"; print HTMLSNP " background-color : #9A9D7C; \n"; print HTMLSNP " }\n"; print HTMLSNP ".tedG { \n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " font-weight : bold;\n"; print HTMLSNP " background-color : #A19EED; \n"; print HTMLSNP " }\n"; print HTMLSNP ".tedG2 { \n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " font-weight : bold;\n"; print HTMLSNP " background-color : #9A9D7C; \n"; print HTMLSNP " }\n"; print HTMLSNP ".final { \n"; print HTMLSNP " border-left:3px;\n"; print HTMLSNP " border-right:0px;\n"; print HTMLSNP " border-top:0px;\n"; print HTMLSNP " border-bottom:0px;\n"; print HTMLSNP " border-style:solid; \n"; print HTMLSNP " border-color:black;\n"; print HTMLSNP " background-color : white; \n"; print HTMLSNP " }\n"; print HTMLSNP ".auto-style1 {"; print HTMLSNP " font-weight: normal;"; print HTMLSNP " font-size: x-small;"; print HTMLSNP "}"; print HTMLSNP "</style>\n"; print HTMLCOUNT "<style type=\"text/css\">\n"; print HTMLCOUNT "th {\n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " border-width:3px;\n"; print HTMLCOUNT " font-family:calibri;\n"; print HTMLCOUNT " }\n"; print HTMLCOUNT "table {\n"; print HTMLCOUNT " margin:auto;\n"; print HTMLCOUNT " border-collapse: collapse;\n"; print HTMLCOUNT " border-width:3px; \n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".th {\n"; print HTMLCOUNT " font-weight : normal;\n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " border-color:white;\n"; print HTMLCOUNT " border-width:0px;\n"; print HTMLCOUNT " font-family:consolas;\n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".tab2 {\n"; print HTMLCOUNT " margin:auto;\n"; print HTMLCOUNT " border-collapse: collapse;\n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " border-width:3px; \n"; print HTMLCOUNT " border-color:white;\n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".tab {\n"; print HTMLCOUNT " margin:auto;\n"; print HTMLCOUNT " border-collapse: collapse;\n"; print HTMLCOUNT " border-width:3px;\n "; print HTMLCOUNT " border-style:solid;\n "; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".td1 { \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " font-size: 11pt;\n"; print HTMLCOUNT " font-family: calibri;\n"; print HTMLCOUNT " border-width:1px;\n"; print HTMLCOUNT " border-left:3px;\n"; print HTMLCOUNT " border-right:3px;\n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " background-color : #c6c3bd; \n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".td2 { \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " font-size: 11pt;\n"; print HTMLCOUNT " font-family: calibri;\n"; print HTMLCOUNT " border-width:1px;\n"; print HTMLCOUNT " border-left:3px;\n"; print HTMLCOUNT " border-right:3px;\n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " background-color : #c6c3ee; \n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".td3 { \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " font-size: 11pt;\n"; print HTMLCOUNT " font-weight: bold;\n"; print HTMLCOUNT " font-family: calibri;\n"; print HTMLCOUNT " border-width:3px;\n"; print HTMLCOUNT " border-left:3px;\n"; print HTMLCOUNT " border-right:3px;\n"; print HTMLCOUNT " border-style:solid; \n"; print HTMLCOUNT " background-color : white; \n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".ted { \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " font-weight : bold;\n"; print HTMLCOUNT " background-color : #A19EED; \n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".ted2 { \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " font-weight : bold;\n"; print HTMLCOUNT " background-color : #9A9D7C; \n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".ted3 { \n"; print HTMLCOUNT " border-color:black;\n"; print HTMLCOUNT " font-family: calibri;\n"; print HTMLCOUNT " color: white;\n"; print HTMLCOUNT " background-color : #333333; \n"; print HTMLCOUNT " }\n"; print HTMLCOUNT ".auto-style1 {"; print HTMLCOUNT " font-weight: normal;"; print HTMLCOUNT " font-size: x-small;"; print HTMLCOUNT "}"; print HTMLCOUNT "</style>\n"; ################################################################################################################################################################################### print HTMLSNP "</head>\n"; print HTMLSNP "<center><img src=\"".$REPimages."SNiPloid7.png\" WIDTH=250></center>"; if ($poly_poly_analysis == 0) { print HTMLSNP "<center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center>"; } print HTMLSNP "<p>\n"; #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- print HTMLCOUNT "</head>\n"; print HTMLCOUNT "<table><tr><td class=\"tab2\"><img src=\"".$REPimages."SNiPloid7.png\" WIDTH=250>"; print HTMLCOUNT "<h3><font face=\"calibri\">Synthesis of the analysis</font></h3></td>"; if ($poly_poly_analysis == 0) { print HTMLCOUNT "<td class=\"tab2\" width=50></td>"; print HTMLCOUNT "<td class=\"tab2\"><table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\">"; print HTMLCOUNT "<tr><th>Diploids</th><th>Polyploid</th><th>Identity</th><th>Interpretation</th></tr>"; print HTMLCOUNT "<tr><td>[1/2]</td><td>[1]</td><td>!=</td><td><img src=\"".$REPimages."1.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[1/2]</td><td>[2]</td><td>!=</td><td><img src=\"".$REPimages."2.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[1]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."3.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[2]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."4.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[1/2]</td><td>[1/2]</td><td>=</td><td><img src=\"".$REPimages."5v.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[1]</td><td>[2]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[1]</td><td>[2/3]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>"; print HTMLCOUNT "<tr><td>[1/2]</td><td>[2/3]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>"; 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>"; 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>"; print HTMLCOUNT "</table></td>"; print HTMLCOUNT "<td class=\"tab2\" width=50></td>"; print HTMLCOUNT "<td class=\"tab2\"><center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center></td>"; #print HTMLCOUNT "<td><table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"><tr><th>Diploids</th><th>Polyploid</th><th>Identity</th><th>Interpretation</th></tr></table></td>"; print HTMLCOUNT "</tr></table>"; } print HTMLCOUNT "<p>\n"; #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- print HTMLSNP "<body>\n"; if ($poly_poly_analysis == 1) { print HTMLSNP "<center><h3><font face=\"calibri\">Result of SNP comparison of two Polyploids</font></h3></center>"; } else { 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>"; } print HTMLSNP "<p>\n"; # COLUMNS - HTMLSNP SNP VIEW print HTMLSNP "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n"; print HTMLSNP "<tr>\n"; print HTMLSNP "<th>Gene</th>"; # (1) Gene print HTMLSNP "<th>Position</th>"; # (2) Position if ($poly_poly_analysis == 1) { print HTMLSNP "<th>REF<br></th>"; print HTMLSNP "<th>Polyploid 1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (3) Polyploid print HTMLSNP "<th>Polyploid 2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (4) Polyploid 2 print HTMLSNP "<th>[Filtered/Total] Depth<br>Polyploid 1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (8) Filtered Depth print HTMLSNP "<th>[Filtered/Total] Depth<br>Polyploid 2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (9) Total Depth # Entęte fichier SNP VIEW TAB print TABSNP "Gene\t"; # (1) Gene print TABSNP "Position\t"; # (2) Position print TABSNP "REF\t"; # (2) Position print TABSNP "Polyploid 1: ".$polyploidName."\t"; # (3) Polyploid print TABSNP "Polyploid 2: ".$genome1Name."\t"; # (4) Genome 1 print TABSNP "P1 Filtered Depth\t"; # (9) Filtered Depth print TABSNP "P1 Total Depth\t"; # (10) Total Depth print TABSNP "P2 Filtered Depth\t"; # (9) Filtered Depth print TABSNP "P2 Total Depth\n"; # (10) Total Depth } else { # (3) Reference print HTMLSNP "<th>Polyploid<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (3) Polyploid print HTMLSNP "<th>Genome 1<br><span class=\"auto-style1\">".$genome1Name."</span></th>"; # (4) Genome 1 print HTMLSNP "<th>Genome 2<br><span class=\"auto-style1\">".$genome2Name."</span></th>"; # (5) Genome 2 print HTMLSNP "<th>Validation</th>"; print HTMLSNP "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>"; # (7) Ratio print HTMLSNP "<th>Filtered<br>Depth</th>"; # (8) Filtered Depth print HTMLSNP "<th>Total<br>Depth</th>"; # (9) Total Depth print HTMLSNP "<th>SNP Class</th>"; # (9) Total Depth # Entęte fichier SNP VIEW TAB print TABSNP "Gene\t"; # (1) Gene print TABSNP "Position\t"; # (2) Position print TABSNP "Polyploid: ".$polyploidName."\t"; # (3) Polyploid print TABSNP "Genome 1: ".$genome1Name."\t"; # (4) Genome 1 print TABSNP "Genome 2: ".$genome2Name."\t"; # (5) Genome 2 print TABSNP "Validation\t"; # (6) Validation print TABSNP "Ratio (%) ".$genome2Name."\t"; # (7) Ratio Genome 1 print TABSNP "Ratio (%) ".$genome1Name."\t"; # (8) Ratio Genome 2 print TABSNP "Filtered Depth\t"; # (9) Filtered Depth print TABSNP "Total Depth\t"; # (10) Total Depth print TABSNP "SNP Class\n"; # (10) Total Depth } print HTMLSNP "</tr>\n"; #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- print HTMLCOUNT "<body>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"; print HTMLCOUNT "<p>\n"; # COLUMNS - HTML SYNTHESIS print HTMLCOUNT "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n"; print HTMLCOUNT "<tr>\n"; print HTMLCOUNT "<th>Gene</th>"; # (1) Gene print HTMLCOUNT "<th>Interval Size<br>Analysed (pb)</th>"; # (2) Interval Size Analyzed print HTMLCOUNT "<th>nb Positions<br>with SNP</th>"; if ($poly_poly_analysis == 0) { # (3) nB Positions With SNP print HTMLCOUNT "<th><img src=\"".$REPimages."1.png\" height=30></th>"; # (4) [1] print HTMLCOUNT "<th><img src=\"".$REPimages."2.png\" height=30></th>"; # (5) [2] print HTMLCOUNT "<th><img src=\"".$REPimages."3ou4.png\" height=30></th>"; # (6) [3 or 4] print HTMLCOUNT "<th><img src=\"".$REPimages."3.png\" height=30></th>"; # (6) [3 or 4] print HTMLCOUNT "<th><img src=\"".$REPimages."4.png\" height=30></th>"; # (6) [3 or 4] print HTMLCOUNT "<th><img src=\"".$REPimages."5v.png\" height=30></th>"; # (11) [5] print HTMLCOUNT "<th><img src=\"".$REPimages."other.png\" height=30></th>"; # (7) [other] print HTMLCOUNT "<th><img src=\"".$REPimages."HG1.png\" height=30><br><span class=\"auto-style1\">".$genome1Name."</span></th>"; # (8) Heterozygosity For Genome 1 print HTMLCOUNT "<th>SNP Intra-Diploids <br><img src=\"".$REPimages."5v.png\" height=30> + <img src=\"".$REPimages."1.png\" height=30> + <img src=\"".$REPimages."2.png\" height=30> + <img src=\"".$REPimages."other.png\" height=30></th>"; # (9) SNP Diploids print HTMLCOUNT "<th>SNP Intra-Polyploid <br> <img src=\"".$REPimages."5v.png\" height=30> + <img src=\"".$REPimages."3ou4.png\" height=30> + <img src=\"".$REPimages."other.png\" height=30></th>"; # (10) SNP Polyploid print HTMLCOUNT "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>\n\n\n\n\n\n\n\n"; # (12) Ratio % print HTMLCOUNT "</tr>\n"; # Entęte HTMLSNP Synthesis print TABCOUNT "Gene\t"; # (1) Gene print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb) print TABCOUNT "nb SNP positions\t"; # (3) nb SNP positions print TABCOUNT "1\t"; # (4) [1] print TABCOUNT "2\t"; # (5) [2] print TABCOUNT "3 or 4\t"; # (6) [3 or 4] print TABCOUNT "3\t"; # (6) [3 or 4] print TABCOUNT "4\t"; # (6) [3 or 4] print TABCOUNT "5\t"; # (11) [5] print TABCOUNT "other\t"; # (7) [other] print TABCOUNT "SNP Heterozygosity Genome 1\t"; # (8) SNP Heterozygosity Genome 1 print TABCOUNT "SNP Diploids\t"; # (9) SNP Diploids print TABCOUNT "SNP Polyploid\t"; # (10) SNP Polyploid print TABCOUNT "Ratio (%) ".$genome2Name."\t"; # (12) Ratio (%) Genome 2 print TABCOUNT "Ratio (%) ".$genome1Name."\n"; # (13) Ratio (%) Genome 1 } else { 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] 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] print HTMLCOUNT "<th>SNP<br>interpolyploids<br>P1 ≠ P2<br><span style=\"auto-style1\"></span></th>"; # (4) [1] #DE8A8A print HTMLCOUNT "<th>P1 ≠ 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] print HTMLCOUNT "<th>P1 ≠ 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] print HTMLCOUNT "<th>P1 ≠ 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] print HTMLCOUNT "<th>P1 ≠ 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] print HTMLCOUNT "<th>SNP<br>intra P1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (4) [1] print HTMLCOUNT "<th>SNP<br>intra P2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (4) [1] print HTMLCOUNT "</tr>\n"; # Entęte HTMLSNP Synthesis print TABCOUNT "Gene\t"; # (1) Gene print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb) print TABCOUNT "nb positions with SNP\t"; # (3) nb SNP positions print TABCOUNT "P1 = P2 [1/2] vs [1/2]\t"; # (4) [1] print TABCOUNT "P1 = P2 [1] vs [1]\t"; # (4) [1] print TABCOUNT "SNP interpolyploids P1 diff P2\t"; # (4) [1] #DE8A8A print TABCOUNT "P1 diff P2 2 Alleles [1] vs [2]\t"; # (4) [1] print TABCOUNT "P1 diff P2 2 Alleles [1/2] vs [1] or [2]\t"; # (4) [1] print TABCOUNT "P1 diff P2 3 Alleles [1/2] vs [3]\t"; # (4) [1] print TABCOUNT "P1 diff P2 3 Alleles [1/2] vs [1/3]\t"; # (4) [1] print TABCOUNT "SNP intra P1 ".$polyploidName."\t" ; # (4) [1] print TABCOUNT "SNP intra P2 ".$polyploid2Name."\n" ; # (4) [1] } #---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- $ligneInter = 0 ; $totalSNP = 0 ; $totalSize = 0 ; $total11 = 0 ; $total22 = 0 ; $total3ou4 = 0 ; $total5 = 0 ; $total512 = 0 ; $total534 = 0 ; $totalOther = 0 ; $totalGenome2 = 0 ; $total3 = 0 ; $total4 = 0 ; $totalNbPolyploid1 = 0 ; # SNP heterozygosity for P1 $totalNbPolyploid2 = 0 ; # SNP heterozygosity for P2 $totalNbCommuns = 0 ; # SNP heterozygosity [P1] = [P2] $totalNbCommunsHomo = 0 ; # SNP homozygosity [P1] = [P2] $totalNbDifferent = 0 ; # [P1] ne [P2] $totalNbHomoDiff = 0 ; # Example : P1 = [A] ; P2 = [G] $totalNbAlleleCommun = 0 ; # Example : P1 = [A/G] ; P2 = [A] $totalAlleleDifferent = 0 ; # Example : P1 = [A/G] ; P2 = [C] or [T] $totalAlleleCommunH = 0 ; # Example : P1 = [A/G] ; P2 = [A/C] } sub int_output { # intern reference foreach my $s(sort(keys(%snp_final))){ ####################################### if ($ligneInter == 0) { print HTMLSNP "<tr class=\"bord1\">\n"; print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n"; } else { print HTMLSNP "<tr class=\"bord2\">\n"; print HTMLCOUNT "<tr class=\"td2\">\n"; } ####################################### my $ref = $snp_final{$s}; my %hash = %$ref; $taille = keys(%hash); # taille de la ligne gene print HTMLSNP "<td rowspan=\"".$taille."\"><b>".$s."</b></td>"; $ligneOK = 0 ; $nbPolyploid = 0; $nbGenomes = 0 ; $nbGenome2 = 0 ; # SNP chez les diploides dans un cas "Other" avec genome 1 heterozygote $nbCommuns = 0; $nbPoly_only = 0 ; $nbSub_only = 0 ; $case5 = 0 ; $case1 = 0 ; $case2 = 0 ; $case3ou4 = 0; $case3 = 0 ; $case4 = 0 ; $caseOther = 0; $casePolyplother = 0 ; # SNP chez le polyploide dans un cas "Other" $caseDiplother = 0 ; # SNP chez les diploides dans un cas "Other" # Moyenne Ponderee $moyenneSNPindep1 = 0 ; $moyenneSNPindep2 = 0 ; @tabTrie = sort ({ $a <=> $b }keys %hash); #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) { foreach my $c(@tabTrie) { if ($ligneOK == 1) { if ($ligneInter == 0) { print HTMLSNP "<tr class=\"td1\">\n"; } else { print HTMLSNP "<tr class=\"td2\">\n"; } } ################################################################################ ### Recuperation des informations ### ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp_final{$s}{$c}); ($DP_P, $FDP) = split(/-/, $DP_P); #print STDOUT "\n($code_snp:$GT_poly) - ($code_G1:$GT_G1)" ; if ($GT_poly ne "") { # Polyploide = [0.0] ou [0.1] ou [1.1] @recupAlleles = split(/\[/,$code_snp); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAltP) = split(/\//,$recupAlleles[0]); # Attribution des alleles au polyploide si pas de SNP if ($GT_poly =~ /^0.0$/) { $code_snp = $alRef ; } if ($GT_poly =~ /^1.1$/) { $code_snp = $alAltP ; } # Attribution des alleles au genome 1 si pas de SNP if (($GT_G1 eq "") || ($GT_G1 =~ /^0.0$/)) { $code_G1 = $alRef ; } if ($GT_G1 =~ /^1.1$/) { @recupAlleles = split(/\[/,$code_G1); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAlt) = split(/\//,$recupAlleles[0]); $code_G1 = $alAlt; } } elsif ($GT_G1 ne "") { # pas de SNP polyploide dans le fichier 1 (fichiers non mergés) -> equivalent de [0.0] @recupAlleles = split(/\[/,$code_G1); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAlt) = split(/\//,$recupAlleles[0]); # Attribution des Alleles au genome 1 if ($GT_G1 =~ /^1.1$/) { $code_G1 = $alAlt ; } if ($GT_G1 =~ /^0.0$/) { $code_G1 = $alRef ; } } ################################################################################ $noSNPpoly = "ok" ; if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) { if ($ligneInter == 0) { print HTMLSNP "<td class=\"tedG2\">".$c."</td>"; print HTMLSNP "<td class=\"ted2\">".$code_snp."</td>"; print HTMLSNP "<td class=\"ted2\">".$code_G1."</td>"; print HTMLSNP "<td class=\"ted2\">".$alRef."</td>"; #REF print HTMLSNP "<td class=\"ted2\">OK</td>"; } else { print HTMLSNP "<td class=\"tedG\">".$c."</td>"; print HTMLSNP "<td class=\"ted\">".$code_snp."</td>"; print HTMLSNP "<td class=\"ted\">".$code_G1."</td>"; print HTMLSNP "<td class=\"ted\">".$alRef."</td>"; #REF print HTMLSNP "<td class=\"ted\">OK</td>"; } } else { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_G1."</td>"; print HTMLSNP "<td>".$alRef."</td>"; #REF print HTMLSNP "<td>not OK</td>"; } print TABSNP $s."\t".$c."\t".$code_snp."\t".$code_G1."\t".$alRef."\t"; $tailleImg = 35 ; if (($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) { # SNP POLYPLOID - [0/1] [0|1] [1|0] # Moyenne du Ratio ----------------------------------- ($sub1,$sub2) = split(",",$ratio); $somme = $sub1 + $sub2 ; if ($somme == 0 ) { print STDOUT "ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\""; die ("ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\""); } else { $ratio = ($sub1/($sub1+$sub2))*100; $ratio = sprintf("%.0f", $ratio); } #$ratio = sprintf("%.0f", $ratio); $ratio2 = 100-$ratio ; #----------------------------------------------------- if (($GT_G1 =~ /^1.1$/)){ # Pas de SNP Genome1 [1/1] [1|1] SNP entre genome1 et genome2 if ($code_G1 eq $alAltP) { # 5 $moyenneSNPindep1 = $moyenneSNPindep1 + $ratio ; $moyenneSNPindep2 = $moyenneSNPindep2 + $ratio2 ; if ($ligneInter == 0) { print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO % print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>"; print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=".$tailleImg."></td>"; } else { print HTMLSNP "<td class=\"ted\">".$ratio.":".$ratio2."<br>"; # RATIO % print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2.">"; # IMG RATIO 2 print HTMLSNP "<td class=\"ted\">".$FDP."</td>"; print HTMLSNP "<td class=\"ted\">".$DP_P."</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=".$tailleImg."></td>"; } print TABSNP "OK\t".$ratio."\t".$ratio2."\t".$FDP."\t".$DP_P."\t5"; $case5 ++ ; } else { # Other 0.1 - 1.1 (O GA A) # Other [SNP DIPLO + SNP POLY] print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother"; $caseOther ++ ; $casePolyplother ++ ; $caseDiplother ++ ; } } else { if (($GT_G1 =~ /^0.0$/)||($GT_G1 =~ /^$/)){ # 3 ou 4 ############################################################################################### # PHASING ############################################################################################### $phasedornot = 0 ; my $is_3 = 0; my $is_4 = 0; if ($GT_poly =~/\|/){ #print STDOUT $s."\n"; my $ref = $phased_regions{$s}; my %hash = %$ref ; foreach my $num_reg(sort(keys(%hash))){ if (exists $phased_regions{$s}{$num_reg}{$c}) { $genotype = $phased_regions{$s}{$num_reg}{$c} ; my $ref2 = $phased_regions{$s}{$num_reg}; my %hash2 = %$ref2 ; foreach my $pos(sort(keys(%hash2))){ if (exists $five{$s}{$pos}){ if (($five{$s}{$pos} =~ /0.1/ && $GT_poly =~ /0.1/) or ($five{$s}{$pos} =~ /1.0/ && $GT_poly =~ /1.0/)){ print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO % print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>"; print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3.png\" height=".$tailleImg."></td>"; $case3 ++ ; $is_3 = 1; } else { print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO % print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>"; print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."4.png\" height=".$tailleImg."></td>"; $case4 ++ ; $is_4 = 1; } $phasedornot = 1 ; last ; } } } } #print STDOUT "\n"; } if ($phasedornot == 0) { print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO % print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>"; print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=".$tailleImg."></td>"; $case3ou4 ++ ; } ############################################################################################### print TABSNP "not OK\t".$ratio."\t".$ratio2."\t".$FDP."\t".$DP_P."\t"; if ($is_3){print TABSNP "3";} elsif ($is_4){print TABSNP "4";} else{print TABSNP "3or4";} } else { #0/1 # heterozygosity G1 print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother,heterozygosity for genome 1"; $nbGenome2 ++ ; $casePolyplother ++ ; $caseOther ++ ; } } } if (($GT_poly =~ /^1.1$/)) { # POLYPLOID NE REFERENCE - [1/1] if ($GT_G1 && ($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0] print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother,heterozygosity for genome 1"; $nbGenome2 ++ ; $caseOther ++ ; } elsif (!$GT_G1){ # POLYPLOID A/A DIPLOIDS T/T print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother"; $caseOther ++ ; } else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2 if ($GT_G1 =~ /^0.0$/){ # Other [NOTHING] print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother"; $caseOther ++ ; } else { if ($code_G1 eq $alAltP) { # 2 print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\t2"; $case2 ++ ; } else { # Other [SNP DIPLO] print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother"; $caseOther ++ ; $caseDiplother ++ ; } } } } if (($GT_poly =~ /^0.0$/)||($GT_poly =~ /^$/)) { #POLYPLOID == REFERENCE - [0|0] #################################### if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0] print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\tother,heterozygosity for genome 1"; $nbGenome2 ++ ; $caseOther++; } else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2 if ($GT_G1 =~ /^1.1$/){ print HTMLSNP "<td>#</td><td>#</td><td>#</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=".$tailleImg."></td>"; print TABSNP "not OK\t#\t#\t#\t#\t1"; $case1 ++ ; } } } print TABSNP "\n"; print HTMLSNP "</tr>\n"; $ligneOK = 1 ; } if ($ligneInter == 0) { print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">".$s."</td>"; } else { print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">".$s."</td>"; } print TABCOUNT $s."\t"; ####################################### if ($ligneInter == 0) { $ligneInter = 1 ; } else { $ligneInter = 0 ; } ####################################### # Calcul des intervalles # ########################## $taille_totale = 0 ; my $ref = $intervalle2{$s}; my %hash = %$ref; foreach my $interval(keys(%hash)){ my @pos = split(/-/,$interval); $taille_inter = $pos[1]-$pos[0]+1 ; $taille_totale = $taille_totale + $taille_inter; } $total1 = $case5 + $case1 + $case2 + $caseDiplother + $nbGenome2; $total2 = $case5 + $case3ou4 + $casePolyplother; # SYNTHESIS print HTMLCOUNT "<td>".$taille_totale."</td><td style=\"border-left:3px solid black\">".$taille."</td></td>"; print HTMLCOUNT "<td style=\"border-left:3px solid black\">"; print HTMLCOUNT $case1."</td><td>".$case2."</td><td>".$case3ou4."</td><td>"; print HTMLCOUNT $case3."</td><td>".$case4."</td><td>".$case5."</td><td>"; print HTMLCOUNT $caseOther."</td><td style=\"border-left:3px solid black\">".$nbGenome2."</td><td style=\"border-left:3px solid black\">".$total1."</td>"; print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$total2."</td>"; print TABCOUNT $taille_totale."\t".$taille."\t"; print TABCOUNT $case1."\t".$case2."\t".$case3ou4."\t".$case3."\t".$case4."\t".$case5."\t".$caseOther."\t".$nbGenome2."\t".$total1."\t".$total2."\t"; $nbTotGenesAna ++ ; if ($case5 != 0) { $nbTotGenesVal ++ ; if ($ligneInter == 1) { print HTMLCOUNT "<td class=\"ted2\" style=\"border-left:3px solid black\">"; print HTMLCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."<br>"; print HTMLCOUNT "<img src=\"".$REPimages."r1.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep1/$case5).">"; print HTMLCOUNT "<img src=\"".$REPimages."r2.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep2/$case5)."></td>"; } else { print HTMLCOUNT "<td class=\"ted\" style=\"border-left:3px solid black\">"; print HTMLCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."<br>"; print HTMLCOUNT "<img src=\"".$REPimages."r1.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep1/$case5).">"; print HTMLCOUNT "<img src=\"".$REPimages."r2.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep2/$case5)."></td>"; } print TABCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5)."\t".sprintf("%.0f", $moyenneSNPindep2/$case5)."\t"; } else { print HTMLCOUNT "<td style=\"border-left:3px solid black\"></td>"; print TABCOUNT "\t"; } print HTMLCOUNT "</tr>"; print TABCOUNT "\n"; $totalSize = $totalSize + $taille_totale ; $totalSNP = $totalSNP + $taille ; $total11 = $total11 + $case1 ; $total22 = $total22 + $case2 ; $total3ou4 = $total3ou4 + $case3ou4 ; $total3 = $total3 + $case3 ; $total4 = $total4 + $case4 ; $total5 = $total5 + $case5 ; $total512 = $total512 + $total1 ; $total534 = $total534 + $total2 ; $totalOther = $totalOther + $caseOther ; $totalGenome2 = $totalGenome2 + $nbGenome2 ; } ########## MODIF DERNIERE MINUTE ################" print HTMLCOUNT "<tr class=\"td3\">\n<td>"; print HTMLCOUNT $nbTotGenesAna."<td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalSize."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalSNP."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $total11."</td><td>"; print HTMLCOUNT $total22."</td><td>"; print HTMLCOUNT $total3ou4."</td><td>"; print HTMLCOUNT $total3."</td><td>"; print HTMLCOUNT $total4."</td><td>"; print HTMLCOUNT $total5."</td><td>"; print HTMLCOUNT $totalOther."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalGenome2."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $total512."</td><td style=\"border:3px solid black\">"; print HTMLCOUNT $total534."</td><td style=\"border:3px solid black\">"; print HTMLCOUNT $nbTotGenesVal."</td>"; print HTMLCOUNT "</tr>"; print TABCOUNT "$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"; print TABCOUNT "\n"; #################################################### print HTMLSNP "</table>\n"; print HTMLSNP "</html>\n"; close HTMLSNP ; print HTMLCOUNT "</table>\n"; print HTMLCOUNT "</html>\n"; close HTMLCOUNT ; close TABSNP; close TABCOUNT ; tie @array, 'Tie::File', $SNP_count or die ; $array[113] = "<tr><td class=\"ted3\">".$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>"; $array[114] = "<td class=\"ted3\" style=\"border-left:3px solid black\">"; $array[115] = $total11."</td><td class=\"ted3\">".$total22."</td><td class=\"ted3\">".$total3ou4."</td><td class=\"ted3\">"; $array[116] = $total3."</td><td class=\"ted3\">".$total4."</td><td class=\"ted3\">".$total5."</td><td class=\"ted3\">"; $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>"; $array[118] = "<td class=\"ted3\" style=\"border-left:3px solid black\">".$total534."</td><td class=\"ted3\">".$nbTotGenesVal."</td></tr>"; } sub ext_output { # Extern reference print TABCOUNT "Gene;Interval Size Analysed (pb);nb SNP;1;2;3 or 4;5;other;SNP Diploids;SNP Polyploid;Ratio (%) $genome2Name:$genome1Name\n"; foreach my $s(sort(keys(%snp))){ ####################################### if ($ligneInter == 0) { print HTMLSNP "<tr class=\"bord1\">\n"; print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n"; } else { print HTMLSNP "<tr class=\"bord2\">\n"; print HTMLCOUNT "<tr class=\"td2\">\n"; } ####################################### my $ref = $snp{$s}; my %hash = %$ref; $taille = keys(%hash); # taille de la ligne gene print HTMLSNP "<td rowspan=\"$taille\"><b>$s</b></td>"; $ligneOK = 0 ; $nbPolyploid = 0; $nbGenomes = 0 ; $nbCommuns = 0; $nbPoly_only = 0 ; $nbSub_only = 0 ; $case5 = 0 ; $case1 = 0 ; $case2 = 0 ; $case3ou4 = 0; $caseOther = 0; $caseGenome2 = 0 ; #Moyenne Ponderee $moyenneSNPindep1 = 0 ; $moyenneSNPindep2 = 0 ; @tabTrie = sort ({ $a <=> $b }keys %hash); #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) { foreach my $c(@tabTrie) { $nb1 = 0 ; $nb2 = 0 ; $nb3 = 0 ; if ($ligneOK == 1) { if ($ligneInter == 0) { print HTMLSNP "<tr class=\"td1\">\n"; } else { print HTMLSNP "<tr class=\"td2\">\n"; } } ### Recuperation des informations ### ($code_snp,$ratio,$GT_poly,$GT_G1,$GT_G2,$DP_P) = split(/\t/,$snp{$s}{$c}); @recupAlleles = split(/\[/,$code_snp); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAlt) = split(/\//,$recupAlleles[0]); $noSNPpoly = "ok" ; #print STDOUT "\n $c $GT_poly $GT_G1 $GT_G2"; print HTMLSNP "<td>$c</td>"; print TABSNP "$c;"; ##################################################################### # SNP POLYPLOID - [0/1] [0|1] [1|0] ##################################################################### if (($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^1.0$/) ) { # Polyploid [0.1] [1.0] $ratio = sprintf("%.0f", $ratio); $ratio2 = 100-$ratio ; $moyenneSNPindep1 = $moyenneSNPindep1 + $ratio ; $moyenneSNPindep2 = $moyenneSNPindep2 + $ratio2 ; print HTMLSNP "<td>$code_snp</td>"; print TABSNP "$code_snp;"; if (($GT_G1 =~ /^1.1$/)){ # Genome1 [1/1] [1|1] print HTMLSNP "<td>$alAlt</td>"; print TABSNP "$alAlt;"; if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>"; print TABSNP "$alAlt;"; print TABSNP ";"; print TABSNP ";"; print TABSNP ";"; print TABSNP "3 or 4;"; } else { if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0] print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>"; print TABSNP "$alRef"; print TABSNP "OK"; print TABSNP "[$ratio/$ratio2;]"; print TABSNP "$DP_P;"; print TABSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>"; print TABSNP "$code_snp;"; print TABSNP "OK;"; print TABSNP "[$ratio/$ratio2];"; print TABSNP "$DP_P;"; print TABSNP "5';"; } } } else{ if ($GT_G1 =~ /^0.0$/){ # # Genome1 [0/0] [0|0] print HTMLSNP "<td>$alRef</td>"; print TABSNP "$alRef;"; if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>"; print TABSNP "$alAlt;"; print TABSNP "OK;"; print TABSNP "[$ratio/$ratio2];"; print TABSNP ";"; print TABSNP "5;"; } else { if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0] print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>"; print TABSNP "$alRef;"; print TABSNP ";"; print TABSNP ";"; print TABSNP ";"; print TABSNP "3 or 4;"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>"; print TABSNP "$code_snp;"; print TABSNP "OK;"; print TABSNP "[$ratio/$ratio2];"; print TABSNP ";"; print TABSNP "5';"; } } } else { # SNP Genome1 [0/1] [0|1] [1|0] print HTMLSNP "<td>$code_snp</td>"; #REF print HTMLSNP "$code_snp;"; #REF if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>"; print TABSNP "$alAlt;"; print TABSNP "OK;"; print TABSNP "[$ratio/$ratio2];"; print TABSNP ";"; print TABSNP "5'"; } else { if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0] print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>"; print TABSNP "$alRef;"; print TABSNP "OK;"; print TABSNP "[$ratio/$ratio2];"; print TABSNP ";"; print TABSNP "5';"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>"; print TABSNP "$code_snp;"; print TABSNP ";"; print TABSNP ";"; print TABSNP ";"; print TABSNP "5''"; } } } print TABSNP "\n"; $ligneOK = 1 ; print HTMLSNP "</tr>\n"; } } ##################################################################### # POLYPLOID NE REFERENCE - [1/1] ##################################################################### #print STDOUT "GTPOLY:$GT_poly@"; if (($GT_poly =~ /^1.1$/) ) { print HTMLSNP "<td>$alAlt</td>"; print TABSNP "$alAlt;"; #################################### if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # Genome 1 [0/1] [0|1] [1|0] print HTMLSNP "<td>$code_snp</td>"; print TABSNP "$code_snp"; if ($GT_G2 =~ /^1.1$/) { print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>"; print TABSNP "$alAlt;;;;5' or 1;"; } else { if ($GT_G2 =~ /^0.0$/) { print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>"; print TABSNP "$altRef;;;;5' or 1;"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>"; print TABSNP "$code_snp;;;;5'';"; } } } else { if ($GT_G1 =~ /^0.0$/){ # Genome1 [0/0] [0|0] ################### print HTMLSNP "<td>$alRef</td>"; print TABSNP "$alRef"; if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=30></td>"; print TABSNP "$alAlt;;;;1;"; } else { if ($GT_G2 =~ /^0.0$/) { print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>"; print TABSNP "$alAlt;;;;3 or 4;"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>"; print TABSNP "$code_snp;;;;5' or 2"; } } } else { # [1/1] [1|1] Genome 1 print HTMLSNP "<td>$alAlt</td>"; print TABSNP "$alAlt"; if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td>$DP_P</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>"; print TABSNP "$alAlt;OK;[$ratio/$ratio2];$DP_P;5;"; } else { if ($GT_G2 =~ /^0.0$/) { print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=30></td>"; print TABSNP "$alRef;;;;2;"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>"; print TABSNP "$code_snp;;;;5' or 2" ; } } } } $nbPolyploid ++ ; print TABSNP "\n"; $ligneOK = 1 ; print HTMLSNP "</tr>\n"; } ##################################################################### # POLYPLOID == REFERENCE - [0|0] ##################################################################### if (($GT_poly =~ /^0.0$/) ) { print HTMLSNP "<td>$alRef</td>"; print TABSNP "$alRef;"; if (($GT_G1 !~ /^0.1$/) && ($GT_G1 !~ /^1.0$/)){ # Genome1 intra [0/1] [0|1] [1|0] print HTMLSNP "<td>$code_snp</td>"; print TABSNP "$code_snp"; if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>"; print TABSNP "$alAlt;;;;5' or 1"; } else { if ($GT_G2 =~ /^0.0$/) { # Genome2 = Ref [0.0] print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>"; print TABSNP "$alRef;;;;5' or 1"; } else { # Genome2 = SNP [0.1] if ( ($GT_G2 =~ /^0.1$/) || ($GT_G2 =~ /^1.0$/)){ # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>"; print TABSNP "$code_snp;;;;5''"; } } } } else { if ($GT_G1 =~ /^0.0$/){ # Pas de SNP Genome1 [0/0] [0|0] print HTMLSNP "<td>$alRef</td>"; print TABSNP "$alRef"; if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=30></td>"; print TABSNP "$alAlt;;;;2;"; } else { if ( ($GT_G2 =~ /^0.1$/) || ($GT_G2 =~ /^1.0$/)){ print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td>OK</td>"; print HTMLSNP "<td>[$ratio/$ratio2]</td>"; print HTMLSNP "<td>$DP_P</td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>"; print TABSNP "$code_snp;OK;[$ratio/$ratio2];$DP_P;5' or 2"; } } } else { # [1/1] [1|1] SNP entre genome1 et genome2 print HTMLSNP "<td>$alAlt</td>"; print TABSNP "$alAlt"; if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1] print HTMLSNP "<td>$alAlt</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=30></td>"; print TABSNP "$alAlt;;;;other;"; } else { if ($GT_G2 =~ /^0.0$/) { print HTMLSNP "<td>$alRef</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=30></td>"; print TABSNP "$alRef;;;;1;"; } else { # Genome2 = SNP [0.1] print HTMLSNP "<td>$code_snp</td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td></td>"; print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>"; print TABSNP "$code_snp;;;;5' or 2;"; } } } } } $nbSub_only ++; print TABSNP "\n"; $ligneOK = 1 ; print HTMLSNP "</tr>\n"; } if ($ligneInter == 0) { print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">$s</td>"; } else { print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">$s</td>"; } 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;"; ####################################### if ($ligneInter == 0) { $ligneInter = 1 ; } else { $ligneInter = 0 ; } ####################################### # Calcul des intervalles $taille_totale = 0 ; my $ref = $intervalle2{$s}; my %hash = %$ref; foreach my $interval(keys(%hash)){ my @pos = split(/-/,$interval); $taille_inter = $pos[1]-$pos[0]-1 ; $taille_totale = $taille_totale + $taille_inter; } $total1 = $case5 + $case1 + $case2 ; $total2 = $case5 + $case3ou4 ; print HTMLCOUNT "<td>$taille_totale</td><td style=\"border-left:3px solid black\">$taille</td></td>"; print HTMLCOUNT "<td style=\"border-left:3px solid black\">$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\">$total2</td>"; if ($case5 != 0) { print HTMLCOUNT "<td style=\"border-left:3px solid black\">".sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."</td>"; } else { print HTMLCOUNT "<td style=\"border-left:3px solid black\"></td>"; } print HTMLCOUNT "</tr>"; $totalSize = $totalSize + $taille_totale ; $totalSNP = $totalSNP + $taille ; $total11 = $total11 + $case1 ; $total22 = $total22 + $case2 ; $total3ou4 = $total3ou4 + $case3ou4 ; $total5 = $total5 + $case5 ; $total512 = $total512 + $total1 ; $total534 = $total534 + $total2 ; $totalOther = $totalOther + $caseOther ; $totalGenome2 = $totalGenome2 + $caseGenome2 ; } ########## MODIF DERNIERE MINUTE ################" print HTMLCOUNT "<tr class=\"td3\">\n"; print HTMLCOUNT "<td></td><td style=\"border-left:3px solid black\">$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>"; print HTMLCOUNT "</tr>"; #################################################### print HTMLSNP "</table>\n"; print HTMLSNP "</html>\n"; print HTMLCOUNT "</table>\n"; print HTMLCOUNT "</html>\n"; close TABSNP; close HTMLSNP ; close HTMLCOUNT ; } sub poly_poly_output { foreach my $s(sort(keys(%snp_final))){ ####################################### if ($ligneInter == 0) { print HTMLSNP "<tr class=\"bord1\">\n"; print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n"; } else { print HTMLSNP "<tr class=\"bord2\">\n"; print HTMLCOUNT "<tr class=\"td2\">\n"; } ####################################### my $ref = $snp_final{$s}; my %hash = %$ref; $taille = keys(%hash); # taille de la ligne gene print HTMLSNP "<td rowspan=\"".$taille."\"><b>".$s."</b></td>"; $ligneOK = 0 ; $nbPolyploid1 = 0 ; # SNP heterozygosity for P1 $nbPolyploid2 = 0 ; # SNP heterozygosity for P2 $nbCommuns = 0 ; # SNP heterozygosity [P1] = [P2] $nbCommunHomo = 0 ; # SNP homozygosity [P1] = [P2] $nbDifferent = 0 ; # [P1] ne [P2] $alleleCommun = 0 ; # Example : P1 = [A/G] ; P2 = [A] $alleleDifferent = 0 ; # Example : P1 = [A/G] ; P2 = [C] or [T] $alleleCommunH = 0 ; # Example : P1 = [A/G] ; P2 = [A/C] $nbHomoDiff = 0 ; @tabTrie = sort ({ $a <=> $b }keys %hash); $taille = 0; #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) { foreach my $c(@tabTrie) { if ($ligneOK == 1) { if ($ligneInter == 0) { print HTMLSNP "<tr class=\"td1\">\n"; } else { print HTMLSNP "<tr class=\"td2\">\n"; } } #print STDOUT "\n\n\n".$snp_final{$s}{$c} ; ($code_snp,$AD,$GT_poly,$DP_P,$code_snp2,$AD_2,$GT_poly2,$DP_P2) = split(/\t/,$snp_final{$s}{$c}); ($DP_P, $FDP) = split(/-/, $DP_P); ($DP_P2, $FDP2) = split(/-/, $DP_P2); #print STDOUT "\nALLELES :".$AD." - ".$AD_2; ($sub1_1,$sub1_2) = split(",",$AD); ($sub2_1,$sub2_2) = split(",",$AD_2); # $sub1_1 = sprintf("%.0f", $sub1_1); # $sub1_2 = sprintf("%.0f", $sub1_2); # $sub2_1 = sprintf("%.0f", $sub2_1); # $sub2_2 = sprintf("%.0f", $sub2_2); if ($DP_P > 0) { $SG1 = ($sub1_1/$DP_P*100) ; $SG2 = ($sub1_2/$DP_P*100) ; } if ($DP_P2 > 0) { $SG3 = ($sub2_1/$DP_P2*100) ; $SG4 = ($sub2_2/$DP_P2*100) ; } if ($GT_poly ne "") { # Polyploide 1 = [0.0] ou [0.1] ou [1.1] @recupAlleles = split(/\[/,$code_snp); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAltP) = split(/\//,$recupAlleles[0]); # Attribution des alleles au polyploide 1 si pas de SNP if ($GT_poly =~ /^0.0$/) { $code_snp = $alRef ; } if ($GT_poly =~ /^1.1$/) { $code_snp = $alAltP ; } # Attribution des alleles au polyploide 2 si pas de SNP if (($GT_poly2 eq "") || ($GT_poly2 =~ /^0.0$/)) { $code_snp2 = $alRef ; } if ($GT_poly2 =~ /^1.1$/) { @recupAlleles = split(/\[/,$code_snp2); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAlt2) = split(/\//,$recupAlleles[0]); $code_snp2 = $alAlt2 ; } } elsif ($GT_poly2 ne "") { # pas de SNP polyploide 1 dans le fichier 1 (fichiers non mergés) -> equivalent de [0.0] @recupAlleles = split(/\[/,$code_snp2); @recupAlleles = split(/\]/,$recupAlleles[1]); ($alRef,$alAlt2) = split(/\//,$recupAlleles[0]); # Attribution des Alleles au polyploide 2 if ($GT_poly2 =~ /^1.1$/) { $code_snp2 = $alAlt2 ; } if ($GT_poly2 =~ /^0.0$/) { $code_snp2 = $alRef ; } } #print STDOUT "\n($code_snp:$GT_poly) - ($code_snp2:$GT_poly2)" ; $noSNPpoly = "ok" ; #____________________________________________________________________________________________________________________________________________ # [1] P1 = 0/1 ; P2 = 0/1 (2 alleles) #print STDOUT "\n".($code_snp2 eq $code_snp); if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_poly2 =~ /^0.1$/)||($GT_poly2 =~ /^1.0$/))) { if (($SG1 > $value_filter_p1) && ($SG2 > $value_filter_p1) && ($SG3 > $value_filter_p2) && ($SG4 > $value_filter_p2) && $code_snp2 eq $code_snp) { if ($ligneInter == 0) { print HTMLSNP "<td class=\"tedG2\">".$c."</td>"; print HTMLSNP "<td class=\"tedG2\">".$alRef."</td>"; print HTMLSNP "<td class=\"ted2\">".$code_snp."</td>"; print HTMLSNP "<td class=\"ted2\">".$code_snp2."</td>"; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; print HTMLSNP "<td class=\"ted2\">".$FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td class=\"ted2\">".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; } else { # print HTMLSNP "<td class=\"tedG\">".$c."</td>"; print HTMLSNP "<td class=\"tedG\">".$alRef."</td>"; print HTMLSNP "<td class=\"ted\">".$code_snp."</td>"; print HTMLSNP "<td class=\"ted\">".$code_snp2."</td>"; print HTMLSNP "<td class=\"ted\">".$FDP." / ".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td class=\"ted\">".$FDP2." / ".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; } $nbPolyploid1 ++ ; # SNP heterozygosity for P1 $nbPolyploid2 ++ ; # SNP heterozygosity for P2 $nbCommuns ++ ; # SNP heterozygosity [P1] = [P2] $taille++; } else { if (($SG1 > $value_filter_p1) && ($SG2 > $value_filter_p1) && ($SG3 > $value_filter_p2) && ($SG4 > $value_filter_p2)) { if ($alAlt2 ne $alAlt) { # P1 [A/G] P2 [A/C] (3 alleles) print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td style=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; $nbDifferent ++ ; $alleleCommunH ++ ; $taille++; } } } } else { # ALL # COMMON PART #print STDOUT "\nBOUM : ".$SG1." + ".$SG2." + ".$SG3." + ".$SG4 ; #if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1) && ($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) { # print HTMLSNP "<td></td><td></td>"; # [5] P1 = 1/1 ; P2 = 1/1 (1 allele) P1 [A] P2 [A] if (($GT_poly =~ /^1.1$/) && ($GT_poly2 =~ /^1.1$/)) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; #********************************************************************************************************************* if ($code_snp2 eq $code_snp) { $nbCommunHomo ++ ; $taille++; } else { # (2 alleles) P1 [A] P2 [C] $nbDifferent ++ ; $nbHomoDiff ++ ; $taille++; } } # [2] [4] P1 = 0/1 ; P2 = 1/1 if (((($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^0.1$/)) && ($GT_poly2 =~ /^1.1$/))) { if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1)) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; if ($alAlt2 ne $alAlt) { # (2 alleles) P1 [A/G] P2 [G] $nbDifferent ++ ; $alleleCommun ++ ; $nbPolyploid1 ++ ; $taille++; } else { # (3 alleles) P1 [A/G] P2 [C] $nbDifferent ++ ; $alleleDifferent ++ ; $nbPolyploid1 ++ ; $taille++; } } } if ((($GT_poly2 =~ /^0.1$/) || ($GT_poly2 =~ /^0.1$/)) && ($GT_poly =~ /^1.1$/)) { if (($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; if ($alAlt2 ne $alAlt) { # (2 alleles) P1 [A/G] P2 [G] $nbDifferent ++ ; $alleleCommun ++ ; $nbPolyploid2 ++ ; $taille++; } else { # (3 alleles) P1 [A/G] P2 [C] $nbDifferent ++ ; $alleleDifferent ++ ; $nbPolyploid2 ++ ; $taille++; } } } # [3] [7] P1 = 0/1 ; P2 = 0/0 (2 alleles) P1 [A/G] P2 [A] if ((($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^0.1$/)) && (($GT_poly2 =~ /^0.0$/) || ($GT_poly2 eq ""))) { if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1)) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; $nbDifferent ++ ; $alleleCommun ++ ; $nbPolyploid1 ++ ; $taille++; } } if ((($GT_poly2 =~ /^0.1$/) || ($GT_poly2 =~ /^0.1$/)) && (($GT_poly =~ /^0.0$/) || ($GT_poly eq ""))) { if (($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; ############ # HERE P2 # ############ $nbDifferent ++ ; $alleleCommun ++ ; $nbPolyploid2 ++ ; $taille++; } } # [6] [8] P1 = 1/1 ; P2 = 0/0 if (($GT_poly =~ /^1.1$/) && (($GT_poly2 =~ /^0.0$/) || ($GT_poly2 eq ""))) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; $nbDifferent ++ ; $alleleCommun ++ ; $nbPolyploid1 ++ ; $taille++; } if (($GT_poly2 =~ /^1.1$/) && (($GT_poly =~ /^0.0$/) || ($GT_poly eq ""))) { print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>"; print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>"; print HTMLSNP "<td>".$code_snp."</td>"; print HTMLSNP "<td>".$code_snp2."</td>"; print HTMLSNP "<td>".$FDP."/".$DP_P; print TABSNP $s . "\t"; print TABSNP $c . "\t"; print TABSNP $alRef . "\t"; print TABSNP $code_snp . "\t"; print TABSNP $code_snp2 . "\t"; print TABSNP $FDP."/".$DP_P; if (($DP_P) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">"; print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>"; print TABSNP "," . $sub1_1." - ".$sub1_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP $FDP2."/".$DP_P2; print HTMLSNP "<td>".$FDP2."/".$DP_P2; if (($DP_P2) != 0) { print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">"; print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">"; print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>"; print TABSNP "," . $sub2_1." - ".$sub2_2."\t"; } else { print HTMLSNP "</td>"; print TABSNP "\t"; } print TABSNP "\n"; print HTMLSNP "</tr>\n"; $nbDifferent ++ ; $alleleCommun ++ ; $nbPolyploid2 ++ ; $taille++; } #} } #print TABSNP $s."\t".$c."\t".$alRef."\t".$code_snp."\t".$code_snp2."\t".$FDP."\t".$DP_P."\t".$FDP2."\t".$DP_P2; $ligneOK = 1 ; } if (($nbCommuns + $nbCommunHomo + $nbDifferent + $nbHomoDiff + $alleleCommun + $alleleDifferent + $alleleCommunH + $nbPolyploid1 + $nbPolyploid2) > 0 ) { if ($ligneInter == 0) { print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">".$s."</td>"; } else { print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">".$s."</td>"; } print TABCOUNT $s."\t"; ####################################### if ($ligneInter == 0) { $ligneInter = 1 ; } else { $ligneInter = 0 ; } ####################################### # Calcul des intervalles # ########################## $taille_totale = 0 ; my $ref = $intervalle2{$s}; my %hash = %$ref; foreach my $interval(keys(%hash)){ my @pos = split(/-/,$interval); $taille_inter = $pos[1]-$pos[0]+1 ; $taille_totale = $taille_totale + $taille_inter; } $total1 = $case5 + $case1 + $case2 + $casePolyplother; $total2 = $case5 + $case3ou4 + $caseDiplother; # SYNTHESIS print HTMLCOUNT "<td>".$taille_totale."</td><td style=\"border-left:3px solid black\">".$taille. "</td></td>"; print HTMLCOUNT "<td style=\"border-left:3px solid black\">"; print HTMLCOUNT $nbCommuns."</td><td>".$nbCommunHomo."</td><td style=\"border-left:3px solid black\">".$nbDifferent."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $nbHomoDiff."</td><td>".$alleleCommun."</td><td>".$alleleDifferent."</td><td>".$alleleCommunH."</td>"; print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$nbPolyploid1."</td><td>".$nbPolyploid2."</td>"; print TABCOUNT $taille_totale."\t".$taille."\t"; print TABCOUNT $nbCommuns."\t".$nbCommunHomo."\t".$nbDifferent."\t".$nbHomoDiff."\t".$alleleCommun."\t".$alleleDifferent."\t".$alleleCommunH."\t".$nbPolyploid1."\t".$nbPolyploid2."\t"; $nbTotGenesAna ++ ; print HTMLCOUNT "</tr>"; print TABCOUNT "\n"; $totalSize = $totalSize + $taille_totale ; $totalSNP = $totalSNP + $taille ; $totalNbPolyploid1 = $totalNbPolyploid1 + $nbPolyploid1 ; # SNP heterozygosity for P1 $totalNbPolyploid2 = $totalNbPolyploid2 + $nbPolyploid2 ; # SNP heterozygosity for P2 $totalNbCommuns = $totalNbCommuns + $nbCommuns ; # SNP heterozygosity [P1] = [P2] $totalNbCommunsHomo = $totalNbCommunsHomo + $nbCommunHomo ; # SNP homozygosity [P1] = [P2] $totalNbDifferent = $totalNbDifferent + $nbDifferent ; # [P1] ne [P2] $totalNbAlleleCommun = $totalNbAlleleCommun + $alleleCommun ; # Example : P1 = [A/G] ; P2 = [A] $totalAlleleDifferent = $totalAlleleDifferent + $alleleDifferent ; # Example : P1 = [A/G] ; P2 = [C] or [T] $totalAlleleCommunH = $totalAlleleCommunH + $alleleCommunH ; # Example : P1 = [A/G] ; P2 = [A/C] $totalNbHomoDiff = $totalNbHomoDiff + $nbHomoDiff ; # Example : P1 = [A/G] ; P2 = [A/C] } } ########## MODIF DERNIERE MINUTE ################" print HTMLCOUNT "<tr class=\"td3\">\n<td>"; print HTMLCOUNT $nbTotGenesAna."<td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalSize."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalSNP."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalNbCommuns."</td><td>"; print HTMLCOUNT $totalNbCommunsHomo."</td><td>"; print HTMLCOUNT $totalNbDifferent."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalNbHomoDiff."</td><td style=\"border-left:3px solid black\">"; print HTMLCOUNT $totalNbAlleleCommun."</td><td style=\"border:3px solid black\">"; print HTMLCOUNT $totalAlleleDifferent."</td><td style=\"border:3px solid black\">"; print HTMLCOUNT $totalAlleleCommunH."</td><td>"; print HTMLCOUNT $totalNbPolyploid1."</td><td>"; print HTMLCOUNT $totalNbPolyploid2."</td>"; print HTMLCOUNT "</tr>"; print TABCOUNT "$nbTotGenesAna\t$totalSize\t$totalSNP\t$totalNbCommuns\t$totalNbCommunsHomo\t$totalNbDifferent\t$totalNbHomoDiff\t$totalNbAlleleCommun\t$totalAlleleDifferent\t$totalAlleleCommunH\t$totalNbPolyploid1\t$totalNbPolyploid2\t"; print TABCOUNT "\n"; #################################################### print HTMLSNP "</table>\n"; print HTMLSNP "</html>\n"; close HTMLSNP ; print HTMLCOUNT "</table>\n"; print HTMLCOUNT "</html>\n"; close HTMLCOUNT ; close TABSNP; close TABCOUNT ; # tie @array, 'Tie::File', $SNP_count or die ; # $array[82] = "<table class=\"tab2\"><th class=\"th\" style=\"text-align:left;\">"; # $array[83] = "<br>".$nbTotGenesAna." analysed genes"; # $array[84] = "<br>".$nbTotGenesVal." with SNP validation"; # $array[85] = "<br>Analysis performed on ".$totalSize." bp"; # $array[86] = "<br>".$totalSNP." SNP"; # $array[87] = "<br><img src=\"".$REPimages."5v.png\" WIDTH=20> : ".$total5." validated SNP"; # $array[88] = "<br><br><img src=\"".$REPimages."1.png\" WIDTH=20> : ".$total11.""; # $array[89] = "<br><img src=\"".$REPimages."2.png\" WIDTH=20> : ".$total22.""; # $array[90] = "<br><img src=\"".$REPimages."3ou4.png\" WIDTH=20> : ".$total3ou4.""; # $array[91] = "<br>Other SNP types : ".$totalOther.""; # $array[92] = "<br>Heterozygosity for genome 1 : ".$totalGenome2.""; # $array[93] = "<br>SNP between parental genomes (diploids) : ".$total512.""; # $array[94] = "<br>SNP polyploid : ".$total534.""; # $array[95] = "<th class=\"th\"><img src=\"".$REPimages."arbre.png\" WIDTH=400></th></table>"; } $time2 = time ; $tmps = $time2 - $time; print STDOUT "\n\nTemps execution : ".$tmps."\n";