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