Mercurial > repos > dereeper > sniploid
changeset 5:e6d35020d28b draft
Deleted selected files
| author | dereeper |
|---|---|
| date | Sat, 13 Oct 2012 13:49:44 -0400 |
| parents | cd051a7c6956 |
| children | cc85d97aeb55 |
| files | SNiPloid.pl SNiPloid.sh SNiPloid.xml |
| diffstat | 3 files changed, 0 insertions(+), 2775 deletions(-) [+] |
line wrap: on
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--- a/SNiPloid.pl Sat Oct 13 13:48:33 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2617 +0,0 @@ -#!/usr/local/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/"; - -$poly_poly_analysis = 0 ; - -=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 = > \ $heterozygosity , -); - - -# Validation - Samples names - - - -%intervalle1 ; -%intervalle2 ; -%snp = () ; -my %snp_final ; -my %five = () ; -my %phased_regions = () ; - -$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 ($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 ; - - 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]; - $snp_code = "[$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 - # $DP = Total Depth - - ($AC,$AF,$AN,$DP,$DS,$Dels,$HRun,$HaplotypeScore,$MQ,$MQ0,$QD,$SB,$sumGLbyD) = split(";",$depth_recuperation); - - ($sub1,$sub2) = split(",",$AD); - $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", $ratio); - } - - @DP = split ("=",$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 eq "true") { - - 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\"><center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center></td></tr></table>"; -} -print HTMLCOUNT "<p>\n"; -#---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- - -print HTMLSNP "<body>\n"; - -if ($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 - - # 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 (%) ".$genome1Name."\t"; # (8) Ratio Genome 2 - print TABSNP "Filtered Depth\t"; # (9) Filtered Depth - print TABSNP "Total Depth\n"; # (10) Total Depth -} -print HTMLSNP "</tr>\n"; - - - -#---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -print HTMLCOUNT "<body>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n"; -print HTMLCOUNT "<p>\n"; -# COLUMNS - HTML SYNTHESIS -print HTMLCOUNT "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n"; -print HTMLCOUNT "<tr>\n"; -print HTMLCOUNT "<th>Gene</th>"; # (1) Gene -print HTMLCOUNT "<th>Interval Size<br>Analysed (pb)</th>"; # (2) Interval Size Analyzed -print HTMLCOUNT "<th>nb Positions<br>with SNP</th>"; -if ($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."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 Diploids</th>"; # (9) SNP Diploids - print HTMLCOUNT "<th>SNP Polyploid</th>"; # (10) SNP Polyploid - print HTMLCOUNT "<th><img src=\"".$REPimages."5v.png\" height=30></th>"; # (11) [5] - print HTMLCOUNT "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>\n\n\n\n\n\n\n\n"; # (12) Ratio % - - print HTMLCOUNT "</tr>\n"; -# Entęte HTMLSNP Synthesis - print TABCOUNT "Gene\t"; # (1) Gene - print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb) - print TABCOUNT "nb SNP positions\t"; # (3) nb SNP positions - print TABCOUNT "1\t"; # (4) [1] - print TABCOUNT "2\t"; # (5) [2] - print TABCOUNT "3 or 4\t"; # (6) [3 or 4] - print TABCOUNT "3\t"; # (6) [3 or 4] - print TABCOUNT "4\t"; # (6) [3 or 4] - print TABCOUNT "other\t"; # (7) [other] - print TABCOUNT "SNP Heterozygosity Genome 1\t"; # (8) SNP Heterozygosity Genome 1 - print TABCOUNT "SNP Diploids\t"; # (9) SNP Diploids - print TABCOUNT "SNP Polyploid\t"; # (10) SNP Polyploid - print TABCOUNT "5\t"; # (11) [5] - print TABCOUNT "Ratio (%) ".$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></td><td></td><td></td><td></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"; - $case5 ++ ; - } - else { # Other 0.1 - 1.1 (O GA A) # Other [SNP DIPLO + SNP POLY] - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; - print TABSNP "\t\t\t\t\tother"; - $caseOther ++ ; - $casePolyplother ++ ; - $caseDiplother ++ ; - } - } - else { - if (($GT_G1 =~ /^0.0$/)||($GT_G1 =~ /^$/)){ # 3 ou 4 - - ############################################################################################### - # PHASING - ############################################################################################### - $phasedornot = 0 ; - if ($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/ && $GT_poly =~ /1.0/)){ - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3.png\" height=".$tailleImg."></td>"; - $case3 ++ ; - } - else { - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."4.png\" height=".$tailleImg."></td>"; - $case4 ++ ; - } - $phasedornot = 1 ; - last ; - } - } - } - } - print STDOUT "\n"; - } - if ($phasedornot == 0) { - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=".$tailleImg."></td>"; - $case3ou4 ++ ; - } - - ############################################################################################### - - - - - print TABSNP "\t\t\t\t\t3or4"; - - } - else { #0/1 # heterozygosity G1 - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>"; - print TABSNP "\t\t\t\t\theterozygosity for genome 1"; - $nbGenome2 ++ ; - $casePolyplother ++ ; - } - } - } - - if (($GT_poly =~ /^1.1$/)) { # POLYPLOID NE REFERENCE - [1/1] - if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0] - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; - print TABSNP "\t\t\t\t\tother"; - $nbGenome2 ++ ; - } - else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2 - if ($GT_G1 =~ /^0.0$/){ # Other [NOTHING] - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; - print TABSNP "\t\t\t\t\tother"; - $caseOther ++ ; - } - else { - if ($code_G1 eq $alAltP) { # 2 - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=".$tailleImg."></td>"; - print TABSNP "\t\t\t\t\t2"; - $case2 ++ ; - } - else { # Other [SNP DIPLO] - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; - print TABSNP "\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$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0] - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>"; - print TABSNP "\t\t\t\t\tother"; - $nbGenome2 ++ ; - } - else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2 - if ($GT_G1 =~ /^1.1$/){ - print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=".$tailleImg."></td>"; - print TABSNP "\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 + $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 $case1."</td><td>".$case2."</td><td>".$case3ou4."</td><td>"; - print HTMLCOUNT $case3."</td><td>".$case4."</td><td>"; - print HTMLCOUNT $caseOther."</td><td>".$nbGenome2."</td><td style=\"border-left:3px solid black\">".$total1."</td>"; - print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$total2."</td><td>".$case5."</td>"; - print TABCOUNT $taille_totale."\t".$taille."\t"; - print TABCOUNT $case1."\t".$case2."\t".$case3ou4."\t".$case3."\t".$case4."\t".$caseOther."\t".$nbGenome2."\t".$total1."\t".$total2."\t".$case5."\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 $totalOther."</td><td>"; - 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 $total5."</td><td>"; - print HTMLCOUNT $nbTotGenesVal."</td>"; - - print HTMLCOUNT "</tr>"; - - - print TABCOUNT "$nbTotGenesAna\t$totalSize\t$totalSNP\t$total11\t$total22\t$total3ou4\t$total3\t$total4\t$totalOther\t$totalGenome2\t$total512\t$total534\t$total5\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\">"; - $array[117] = $totalOther."</td><td class=\"ted3\">".$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\">".$total5."</td><td class=\"ted3\">".$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";
--- a/SNiPloid.sh Sat Oct 13 13:48:33 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -#!/bin/bash - - -directory=`dirname $0` - -if [ -d "$HOME/galaxy_dist/static/images" ]; then - cp -rf $directory/img_sniploid $HOME/galaxy_dist/static/images -fi -if [ -d "$HOME/galaxy-dist/static/images" ]; then - cp -rf $directory/img_sniploid $HOME/galaxy-dist/static/images -fi - - -if [ "$1" = "poly" ] # poly analysis -then - perl $directory/SNiPloid.pl --dp $2 --dp2 $3 --vp $4 --cpp $5 --vp2 $6 --cpp2 $7 --oc $8 --oh $9 --ohs ${10} --ocs ${11} --elq ${12} --vfp1 ${14} --vfp2 ${15} --img ../../../static/images/img_sniploid/ 2>&1 >>${13} -elif [ $2 -eq 0 ] # Ref ext -then - perl $directory/SNiPloid.pl --dp $3 --dg1 $4 --vp $5 --cpp $6 --vg1 $7 --cg1 $8 --dg2 $9 --vg2 $10 --cg2 $11 -- ref 0 --oc ${12} --oh ${13} --ohs ${14} --ocs ${15} --elq ${16} --img ../../../static/images/img_sniploid/ 2>&1 >>${17} -else # Ref int == 1 - perl $directory/SNiPloid.pl --gn2 $3 --dp $4 --dg1 $5 --vp $6 --cpp $7 --vg1 $8 --cg1 $9 --ref 1 --oc ${10} --oh ${11} --ohs ${12} --ocs ${13} --elq ${14} --img ../../../static/images/img_sniploid/ 2>&1 >>${15} -fi
--- a/SNiPloid.xml Sat Oct 13 13:48:33 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,136 +0,0 @@ -<tool id="SNiPloid" name="SNiPloid"> - <description>Comparison of SNP between a Tetraploid and its Parental Genomes</description> - <command interpreter="bash">./SNiPloid.sh - $Poly_Analysis.polyornot <!-- $1 --> - #if $Poly_Analysis.polyornot == "poly": - - $Poly_Analysis.depthPolyploid1 $Poly_Analysis.depthPolyploid2 <!-- $4 $5 --> - $Poly_Analysis.VCFpolyploid1 $Poly_Analysis.DOCpolyploid1 <!-- $6 $7 --> - $Poly_Analysis.VCFpolyploid2 $Poly_Analysis.DOCpolyploid2 <!-- $8 $9 --> - #else: - $Poly_Analysis.Reference.ref <!-- $2 --> - - #if $Poly_Analysis.Reference.ref == "1": - $Poly_Analysis.Reference.genome2Name - #end if - - $Poly_Analysis.Reference.depthPolyploid1 $Poly_Analysis.Reference.depthGenome1 <!-- $6 $7 --> - $Poly_Analysis.Reference.VCFpolyploid1 $Poly_Analysis.Reference.DOCpolyploid1 <!-- $8 $9 --> - $Poly_Analysis.Reference.VCFgenome1 $Poly_Analysis.Reference.DOCgenome1 <!-- $10 $11 --> - #if $Poly_Analysis.Reference.ref == "0": - $Poly_Analysis.Reference.depthGenome2 <!-- $12 --> - $Poly_Analysis.Reference.VCFgenome2 $Poly_Analysis.Reference.DOCgenome2 <!-- $13 $14 --> - #end if - #end if - $SNP_csv $SNP_html $SNP_count $SNP_count_csv $enableLowQuality $log - #if $Poly_Analysis.polyornot == "poly": - $Poly_Analysis.value_filter_p1 $Poly_Analysis.value_filter_p2 - #end if - </command> - - <inputs> - - <conditional name="Poly_Analysis"> - - <param type="select" name="polyornot" label="Type of analysis"> - <option value="poly" selected="True">POLYPLOID vs POLYPLOID</option> - <option value="notpoly">POLYPLOID vs PARENTAL DIPLOID GENOMES</option> - </param> - - <when value="poly"> - <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid 1)" value="20"/> - <param type="text" name="depthPolyploid2" label="Minimum read depth at a position to make a call (Polyploid 2)" value="20"/> - <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid 1)"/> - <param format="vcf" name="VCFpolyploid2" type="data" label="VCF file (Polyploid 2)"/> - <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid 1)"/> - <param format="coverage" name="DOCpolyploid2" type="data" label="Depth of coverage information (Polyploid 2)"/> - <param type="text" name="value_filter_p1" label="Minimum minor allele frequency (in %) (Polyploid 1)" value="10"/> - <param type="text" name="value_filter_p2" label="Minimum minor allele frequency (in %) (Polyploid 2)" value="10"/> - </when> - - <when value="notpoly"> - <conditional name="Reference"> - - <param type="select" name="ref" label="Reference" help="INTERN (Genome 2 as reference) or EXTERN"> - <option value="1" selected="True">INTERN</option> - <option value="0">EXTERN</option> - </param> - - <when value="0"> - <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/> - <param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/> - <param type="text" name="depthGenome2" label="Minimum read depth at a position to make a call (Genome 2)" value="20"/> - <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/> - <param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)"/> - <param format="vcf" name="VCFgenome2" type="data" label="VCF file (Genome 2)"/> - <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/> - <param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/> - <param format="coverage" name="DOCgenome2" type="data" label="Depth of coverage information (Genome2)"/> - </when> - - <when value="1"> - <param type="text" name="genome2Name" label="Genome 2 Name (Reference)" value="GenomeName"/> - <param type="text" name="depthPolyploid1" label="Minimum read depth at a position to make a call (Polyploid)" value="20"/> - <param type="text" name="depthGenome1" label="Minimum read depth at a position to make a call (Genome 1)" value="20"/> - <param format="vcf" name="VCFpolyploid1" type="data" label="VCF file (Polyploid)"/> - <param format="vcf" name="VCFgenome1" type="data" label="VCF file (Genome 1)" help="VCF file with [Genome 1] vs. [Genome 2] as Reference. /!\ Lost of heterozygosity for [Genome 2]"/> - <param format="coverage" name="DOCpolyploid1" type="data" label="Depth of coverage information (Polyploid)"/> - <param format="coverage" name="DOCgenome1" type="data" label="Depth of coverage information (Genome 1)"/> - </when> - - </conditional> - - </when> - - </conditional> - - - - <param name="enableLowQuality" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Enable LowQual SNP ?" help="Default : only PASS SNP are considered" /> - - - </inputs> - - <outputs> - - <data format="txt" name="SNP_csv" label="SNP output" /> - <data format="html" name="SNP_html" label="SNP output (HTML)" /> - <data format="html" name="SNP_count" label="Synthesis output (HTML)" /> - <data format="txt" name="SNP_count_csv" label="Synthesis output" /> - <data format="txt" name="log" label="log" /> - - </outputs> - - <help> -.. class:: infomark - -**Program encapsulated in Galaxy by Southgreen** - -.. class:: infomark - -**SNiPlay utilities** - ------ - -============== - Authors: -============== - -**Marine Peralta** - - ------ - -========== - Overview -========== - -SNiPloid... ------ - - - - - </help> - -</tool>