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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 ($name_gene ne $gene_pre)
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306 {
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307 if ($rec == 1) {
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308 $position_fin = $position_pre ;
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309 $val_fin = $val_deb.$position_fin ; # Intervalle end position
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310 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
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311 }
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312 $rec = 0;
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313 }
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314 if ($depthcov >= $depthPolyploid){
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315 if ($rec == 0) {
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316 $position_deb = $position[1] ;
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317 $val_deb = $position_deb."-"; # Intervalle start position
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318 }
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319 $rec = 1 ;
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320 }
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321 if ($depthcov < $depthPolyploid){
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322 if ($rec == 1) {
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323 $position_fin = $position_pre ;
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324 $val_fin = $val_deb.$position_fin ; # Intervalle end position
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325 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
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326 }
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327 $rec = 0;
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328 }
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329
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330 }
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331 }
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332 else { # Merged files (2 or 3 species)
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333 if ($ref == 0) { # 3 species
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334 $depthcov1 = $ligne[$indiceGenome2] ;
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335 $depthcov2 = $ligne[$indicePolyploid1] ;
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336 $depthcov3 = $ligne[$indiceGenome1] ;
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337 if ($name_gene){
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338 if (($depthcov1 >= $depthGenome2) && ($depthcov2 >= $depthPolyploid)&& ($depthcov3 >= $depthGenome1)){
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339 if ($rec == 0) {
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340 $position_deb = $position[1] ;
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341 $val_deb = $position_deb."-";
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342 }
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343 $rec = 1 ;
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344 }
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345 if (($depthcov1 < $depthGenome2) || ($depthcov2 < $depthPolyploid) || ($depthcov3 < $depthGenome1)){
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346 if ($rec == 1) {
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347 $position_fin = $position_pre ;
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348 $val_fin = $val_deb.$position_fin ;
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349 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
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350 }
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351 $rec = 0 ;
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352 }
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353 }
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354 }
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355 else { # 2 species
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356 $depthcov1 = $ligne[$indicePolyploid1] ;
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357 $depthcov2 = $ligne[$indiceGenome1] ;
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358 if ($name_gene){
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359 if (($depthcov1 >= $depthPolyploid) && ($depthcov2 >= $depthGenome1)){
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360 if ($rec == 0) {
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361 $position_deb = $position[1] ;
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362 $val_deb = $position_deb."-";
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363 }
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364 $rec = 1 ;
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365 }
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366 if (($depthcov1 < $depthPolyploid) || ($depthcov2 < $depthGenome1)){
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367 if ($rec == 1) {
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368 $position_fin = $position_pre ;
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369 $val_fin = $val_deb.$position_fin ;
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370 $intervalle1{$gene_pre}{$val_fin} = "ok" ;
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371 }
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372 $rec = 0 ;
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373 }
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374 }
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375 }
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376 }
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377 $position_pre = $position[1] ;
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378 $gene_pre = $name_gene ;
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379 }
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380 }
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381 return (%intervalle1) ;
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382
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383 }
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384 sub Intervall_part2 {
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385
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386 my(@args) = @_;
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387 #print "\nintervall part 2 : $args[1]";
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388
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389 open (TABSNP, $args[0]) or die ("Pbm a l'ouverture du fichier : $args[0]");
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390 #print STDOUT "\n$args[0]";
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391 @DOC = <TABSNP> ;
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392 my %tab ;
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393 foreach $li(@DOC) {
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394 if ($li =~ /^(.+):(.+)\t(.+)\t.+\t.+$/) {
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395 $tab{$1}{$2} = $3;
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396 }
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397 }
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398 close TABSNP ;
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399
|
|
|
400
|
|
|
401
|
|
|
402 $rec = 0 ;
|
|
|
403 $position_pre ;
|
|
|
404 $val_deb = "";
|
|
|
405 $val_fin = "";
|
|
|
406
|
|
|
407 foreach my $interval(sort (keys(%intervalle1))){
|
|
|
408
|
|
|
409 my $ref = $intervalle1{$interval};
|
|
|
410 my %intervalls = %$ref;
|
|
|
411 $name_gene = $interval ;
|
|
|
412
|
|
|
413 foreach my $intervall(sort (keys(%intervalls))){
|
|
|
414 $final = 2 ;
|
|
|
415 $rec = 0 ;
|
|
|
416 ($debut,$fin) = split(/-/,$intervall);
|
|
|
417 for ($i=$debut; $i <=$fin; $i++) {
|
|
|
418 if ($tab{$interval}{$i} >= $args[1]){
|
|
|
419 if ($rec == 0) {
|
|
|
420 $position_deb = $i ;
|
|
|
421 $val_deb = $position_deb."-";
|
|
|
422 }
|
|
|
423 $rec = 1 ;
|
|
|
424 $final = 0 ;
|
|
|
425 }
|
|
|
426 if ($tab{$interval}{$i} < $args[1]){
|
|
|
427 $final = 1 ;
|
|
|
428 if ($rec == 1) {
|
|
|
429 $position_fin = $i-1 ;
|
|
|
430 $val_fin = $val_deb.$position_fin ;
|
|
|
431 $intervalle2{$name_gene}{$val_fin} = "ok" ;
|
|
|
432 }
|
|
|
433 $rec = 0 ;
|
|
|
434 }
|
|
|
435 }
|
|
|
436 if ($final == 0) {
|
|
|
437 $val_fin = $val_deb.$fin ;
|
|
|
438 $intervalle2{$name_gene}{$val_fin} = "ok" ;
|
|
|
439 }
|
|
|
440 }
|
|
|
441 }
|
|
|
442 if ($VCFgenome2 ne ""){
|
|
|
443 %intervalle1 = %intervalle2 ;
|
|
|
444 }
|
|
|
445
|
|
|
446 foreach my $interval(sort (keys(%intervalle2))){
|
|
|
447 my $ref = $intervalle2{$interval};
|
|
|
448 my %intervalls = %$ref;
|
|
|
449 $name_gene = $interval ;
|
|
|
450 }
|
|
|
451 return (%intervalle2) ;
|
|
|
452 }
|
|
|
453
|
|
|
454 sub VCF_Analysis {
|
|
|
455 %snp_final = () ;
|
|
|
456 $compt_phasing = 0 ;
|
|
|
457 $compt_five = 0 ;
|
|
|
458 my(@args) = @_;
|
|
|
459
|
|
|
460 open (TABSNP, "$args[0]") or die ("ERROR : file $args[0] don't exists");
|
|
|
461 @VCF = <TABSNP> ;
|
|
|
462 close TABSNP ;
|
|
|
463
|
|
|
464 ###########################################
|
|
|
465 # test if VCF was filtered
|
|
|
466 ###########################################
|
|
|
467 my $vcf_file = $args[0];
|
|
|
468 my $grep_pass = `grep -c 'PASS' $vcf_file`;
|
|
|
469 chomp($grep_pass);
|
|
|
470 my $pass = "PASS";
|
|
|
471 if (defined $grep_pass && $grep_pass == 0)
|
|
|
472 {
|
|
|
473 $pass = ".";
|
|
|
474 }
|
|
|
475
|
|
|
476 #print "$pass $grep_pass $vcf_file\n";
|
|
|
477
|
|
|
478 foreach $line(@VCF){
|
|
|
479 if ($line =~ /^#CHROM.+FORMAT\t(.+)$/) {
|
|
|
480 $name_record = $1 ;
|
|
|
481 }
|
|
|
482 if ($line !~ /^#/){
|
|
|
483 @infos_line = split(/\t/,$line) ;
|
|
|
484 $gene = $infos_line[0];
|
|
|
485 $position = $infos_line[1];
|
|
|
486 $ref_allele = $infos_line[3];
|
|
|
487 $alt_allele = $infos_line[4];
|
|
|
488
|
|
|
489 if ($ref_allele =~/\w\w/ or $alt_allele =~/\w\w/)
|
|
|
490 {
|
|
|
491 next;
|
|
|
492 }
|
|
|
493
|
|
|
494 $snp_code = "[$ref_allele/$alt_allele]";
|
|
|
495 $quality_of_snp = $infos_line[6];
|
|
|
496 $depth_recuperation = $infos_line[7];
|
|
|
497 $alleles = $infos_line[9];
|
|
|
498
|
|
|
499 ($GT,$AD,$FDP,$GQ,$PL) = split(":",$alleles);
|
|
|
500
|
|
|
501
|
|
|
502 # PHASING
|
|
|
503
|
|
|
504 if (($GT =~ /\|/) && ($previous_GT =~ /\//)) { # initialisation région
|
|
|
505 $compt_phasing ++ ;
|
|
|
506 $phased_regions{$gene}{$compt_phasing}{$previous_position} = $previous_GT ;
|
|
|
507 $phased_regions{$gene}{$compt_phasing}{$position} = $GT ;
|
|
|
508 }
|
|
|
509 if (($GT =~ /\|/) && ($previous_GT =~ /\|/)) { # extension région
|
|
|
510 $phased_regions{$gene}{$compt_phasing}{$position} = $GT ;
|
|
|
511 }
|
|
|
512
|
|
|
513
|
|
|
514 # $FDP = Filtered Depth
|
|
|
515 # $DP = Total Depth
|
|
|
516
|
|
|
517 my $DP;
|
|
|
518 my @tags = split(";",$depth_recuperation);
|
|
|
519 foreach my $tag(@tags)
|
|
|
520 {
|
|
|
521 if ($tag =~/DP=/)
|
|
|
522 {
|
|
|
523 $DP = $tag;
|
|
|
524 }
|
|
|
525 }
|
|
|
526
|
|
|
527 #($sub1,$sub2) = split(",",$AD);
|
|
|
528 #$somme = $sub1 + $sub2 ;
|
|
|
529
|
|
|
530 $somme = 0;
|
|
|
531 my @depth_of_alleles = split(",",$AD);
|
|
|
532 my $sub1 = $depth_of_alleles[0];
|
|
|
533 foreach my $depth_of_allele(@depth_of_alleles)
|
|
|
534 {
|
|
|
535 $somme += $depth_of_allele;
|
|
|
536 }
|
|
|
537
|
|
|
538
|
|
|
539
|
|
|
540 if ($somme == 0 ) {
|
|
|
541 print STDOUT "ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"";
|
|
|
542 die ("ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"");
|
|
|
543 }
|
|
|
544 else {
|
|
|
545 $ratio = ($sub1/$somme)*100;
|
|
|
546 $ratio = sprintf("%.0f", $ratio);
|
|
|
547 }
|
|
|
548
|
|
|
549 @DP = split ("=",$DP) ;
|
|
|
550
|
|
|
551 $test_inside_interval = 0 ;
|
|
|
552
|
|
|
553 my $ref = $intervalle2{$gene};
|
|
|
554 my %hash = %$ref;
|
|
|
555
|
|
|
556 foreach my $interval(keys(%hash)){
|
|
|
557 my @pos = split(/-/,$interval) ;
|
|
|
558 if ($position >= $pos[0] && $position <= $pos[1]) {
|
|
|
559 $test_inside_interval = 1 ;
|
|
|
560 last ;
|
|
|
561 }
|
|
|
562 }
|
|
|
563 # ENABLE LOW_QUALITY SNP
|
|
|
564 if ($enableLowQuality == 1) {
|
|
|
565 if ($test_inside_interval == 1 ){ #
|
|
|
566 if ($args[0] eq $VCFpolyploid) { # Polyploid
|
|
|
567 $polyploidName = $name_record ;
|
|
|
568 $snp{$gene}{$position} = $snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
|
|
|
569 }
|
|
|
570 else {
|
|
|
571 if ($args[0] eq $VCFgenome1) { # genome1
|
|
|
572 $genome1Name = $name_record ;
|
|
|
573 if (exists $snp{$gene}{$position}) { # if polyploid SNP
|
|
|
574 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT ;
|
|
|
575
|
|
|
576 ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp{$gene}{$position});
|
|
|
577 @recupAlleles = split(/\[/,$code_snp);
|
|
|
578 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
579 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
|
|
|
580 @recupAlleles = split(/\[/,$code_G1);
|
|
|
581 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
582 ($alRef,$code_G1) = split(/\//,$recupAlleles[0]);
|
|
|
583
|
|
|
584 #print "\nINFOS\n".$GT_poly."\t";
|
|
|
585 #print $GT_G1."\t";
|
|
|
586 #print $code_G1."\t";
|
|
|
587 #print $alAltP."\n";
|
|
|
588 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) {
|
|
|
589 $five{$gene}{$position} = $GT_poly ;
|
|
|
590 }
|
|
|
591 }
|
|
|
592 else { # if no polyploid SNP, key is empty
|
|
|
593 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$GT ;
|
|
|
594 }
|
|
|
595 }
|
|
|
596 else { # genome2
|
|
|
597 if ($args[0] eq $VCFgenome2) {
|
|
|
598 $genome2Name = $name_record ;
|
|
|
599 if (exists $snp{$gene}{$position}) { # if polyploid SNP
|
|
|
600 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT;
|
|
|
601 }
|
|
|
602 else { # if no polyploid SNP and no genome1, key is empty
|
|
|
603 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$ref_allele."\t\t".$snp_code."\t".$GT ;
|
|
|
604 }
|
|
|
605 }
|
|
|
606 }
|
|
|
607 if ($args[0] eq $VCFpolyploid2) { # polyploid2
|
|
|
608 $polyploid2Name = $name_record ;
|
|
|
609 if (exists $snp{$gene}{$position}) { # if polyploid SNP
|
|
|
610 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
|
|
|
611 }
|
|
|
612 else { # if no polyploid SNP, key is empty
|
|
|
613 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
|
|
|
614 }
|
|
|
615 }
|
|
|
616 }
|
|
|
617 }
|
|
|
618 }
|
|
|
619 # ONLY PASS SNP CONSIDERED
|
|
|
620 else {
|
|
|
621 if (($test_inside_interval == 1 ) && ($quality_of_snp eq $pass) && ($snp{$gene}{$position} ne "LQ")){ #
|
|
|
622 if ($args[0] eq $VCFpolyploid) { # Polyploid
|
|
|
623 $polyploidName = $name_record ;
|
|
|
624 $snp{$gene}{$position} = $snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
|
|
|
625 }
|
|
|
626 else {
|
|
|
627 if ($args[0] eq $VCFgenome1) { # genome1
|
|
|
628 $genome1Name = $name_record ;
|
|
|
629 if (exists $snp{$gene}{$position}) { # if polyploid SNP
|
|
|
630 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT ;
|
|
|
631
|
|
|
632 ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp{$gene}{$position});
|
|
|
633 @recupAlleles = split(/\[/,$code_snp);
|
|
|
634 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
635 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
|
|
|
636 @recupAlleles = split(/\[/,$code_G1);
|
|
|
637 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
638 ($alRef,$code_G1) = split(/\//,$recupAlleles[0]);
|
|
|
639
|
|
|
640 #print "\nINFOS\n".$GT_poly."\t";
|
|
|
641 #print $GT_G1."\t";
|
|
|
642 #print $code_G1."\t";
|
|
|
643 #print $alAltP."\n";
|
|
|
644 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) {
|
|
|
645 $five{$gene}{$position} = $GT_poly ;
|
|
|
646 }
|
|
|
647 }
|
|
|
648 else { # if no polyploid SNP, key is empty
|
|
|
649 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$GT ;
|
|
|
650 }
|
|
|
651 }
|
|
|
652 else { # genome2
|
|
|
653 if ($args[0] eq $VCFgenome2) {
|
|
|
654 $genome2Name = $name_record ;
|
|
|
655 if (exists $snp{$gene}{$position}) { # if polyploid SNP
|
|
|
656 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$GT;
|
|
|
657 }
|
|
|
658 else { # if no polyploid SNP and no genome1, key is empty
|
|
|
659 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$ref_allele."\t\t".$snp_code."\t".$GT ;
|
|
|
660 }
|
|
|
661 }
|
|
|
662 }
|
|
|
663 if ($args[0] eq $VCFpolyploid2) { # polyploid2
|
|
|
664 $polyploid2Name = $name_record ;
|
|
|
665 if (exists $snp{$gene}{$position}) { # if polyploid SNP
|
|
|
666 $snp{$gene}{$position} = $snp{$gene}{$position}."\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
|
|
|
667 }
|
|
|
668 else { # if no polyploid SNP, key is empty
|
|
|
669 $snp{$gene}{$position} = $ref_allele."\t\t\t\t".$snp_code."\t".$AD."\t".$GT."\t".$DP[1]."-".$FDP ;
|
|
|
670 }
|
|
|
671 }
|
|
|
672 }
|
|
|
673 }
|
|
|
674 else {
|
|
|
675 if ($quality_of_snp ne $pass) {
|
|
|
676 $snp{$gene}{$position} = "LQ";
|
|
|
677 }
|
|
|
678 }
|
|
|
679 }
|
|
|
680 ################################################################################################################################
|
|
|
681 }
|
|
|
682 $previous_GT = $GT ;
|
|
|
683 $previous_position = $position ;
|
|
|
684 }
|
|
|
685 foreach my $s(sort(keys(%snp))){
|
|
|
686 my $ref = $snp{$s};
|
|
|
687 my %hash = %$ref;
|
|
|
688 foreach my $snip(keys(%hash)){
|
|
|
689 if ($snp{$s}{$snip} ne "LQ"){
|
|
|
690 $snp_final{$s}{$snip} = $snp{$s}{$snip} ;
|
|
|
691 }
|
|
|
692 }
|
|
|
693 }
|
|
|
694 return (%snp_final) ;
|
|
|
695 }
|
|
|
696
|
|
|
697 sub intro_output {
|
|
|
698
|
|
|
699 ###########################################################
|
|
|
700 # ANALYSE - CREATION FICHIERS DE SORTIE #
|
|
|
701 ###########################################################
|
|
|
702
|
|
|
703 # Ouverture des fichiers
|
|
|
704 open (HTMLSNP, ">$SNP_html");
|
|
|
705 open (TABSNP, ">$SNP_csv");
|
|
|
706 open (HTMLCOUNT, ">$SNP_count");
|
|
|
707 open (TABCOUNT, ">$SNP_count_csv");
|
|
|
708
|
|
|
709 print HMTL "<html>\n";
|
|
|
710 print HTMLCOUNT "<html>\n";
|
|
|
711
|
|
|
712 print HTMLSNP "<head>\n";
|
|
|
713 print HTMLCOUNT "<head>\n";
|
|
|
714
|
|
|
715 #####################################################
|
|
|
716 # CSS #
|
|
|
717 #####################################################
|
|
|
718 print HTMLSNP "<style type=\"text/css\">\n";
|
|
|
719
|
|
|
720 print HTMLSNP "th {\n";
|
|
|
721 print HTMLSNP " border-color:black;\n";
|
|
|
722 print HTMLSNP " border-style:solid; \n";
|
|
|
723 print HTMLSNP " border-width:3px;\n";
|
|
|
724 print HTMLSNP " font-family: calibri;\n";
|
|
|
725 print HTMLSNP " }\n";
|
|
|
726
|
|
|
727 print HTMLSNP "body {text-align:center;}\n";
|
|
|
728
|
|
|
729 print HTMLSNP "table {\n";
|
|
|
730 print HTMLSNP " border-color:black;\n";
|
|
|
731 print HTMLSNP " margin:auto;\n";
|
|
|
732 print HTMLSNP " border-collapse: collapse;\n";
|
|
|
733 print HTMLSNP " border-width:3px; \n";
|
|
|
734 print HTMLSNP " border-style:solid; \n";
|
|
|
735 print HTMLSNP " }\n";
|
|
|
736
|
|
|
737 print HTMLSNP ".bord1 { \n";
|
|
|
738
|
|
|
739 print HTMLSNP " font-size: 11pt;\n";
|
|
|
740 print HTMLSNP " font-family: calibri;\n";
|
|
|
741 print HTMLSNP " border-width:1px;\n";
|
|
|
742 print HTMLSNP " border-top:3px;\n";
|
|
|
743 print HTMLSNP " border-left:3px;\n";
|
|
|
744 print HTMLSNP " border-right:3px;\n";
|
|
|
745 print HTMLSNP " border-style:solid; \n";
|
|
|
746 print HTMLSNP " border-color:black;\n";
|
|
|
747 print HTMLSNP " background-color : #c6c3bd; \n";
|
|
|
748 print HTMLSNP " }\n";
|
|
|
749
|
|
|
750 print HTMLSNP ".bord2 { \n";
|
|
|
751
|
|
|
752 print HTMLSNP " font-size: 11pt;\n";
|
|
|
753 print HTMLSNP " font-family: calibri;\n";
|
|
|
754 print HTMLSNP " border-width:1px;\n";
|
|
|
755 print HTMLSNP " border-top:3px;\n";
|
|
|
756 print HTMLSNP " border-left:3px;\n";
|
|
|
757 print HTMLSNP " border-right:3px;\n";
|
|
|
758 print HTMLSNP " border-style:solid; \n";
|
|
|
759 print HTMLSNP " border-color:black;\n";
|
|
|
760 print HTMLSNP " background-color : #c6c3ee; \n";
|
|
|
761 print HTMLSNP " }\n";
|
|
|
762
|
|
|
763
|
|
|
764 print HTMLSNP "td { \n";
|
|
|
765 print HTMLSNP " border-color:black;\n";
|
|
|
766 print HTMLSNP " }\n";
|
|
|
767
|
|
|
768 print HTMLSNP ".tdm { \n";
|
|
|
769 print HTMLSNP " border-color:black;\n";
|
|
|
770 print HTMLSNP " border-left:3px;\n";
|
|
|
771 print HTMLSNP " }\n";
|
|
|
772
|
|
|
773
|
|
|
774 print HTMLSNP ".td1 { \n";
|
|
|
775 print HTMLSNP " border-color:black;\n";
|
|
|
776 print HTMLSNP " font-size: 11pt;\n";
|
|
|
777 print HTMLSNP " font-family: calibri;\n";
|
|
|
778 print HTMLSNP " border-width:1px;\n";
|
|
|
779 print HTMLSNP " border-left:3px;\n";
|
|
|
780 print HTMLSNP " border-right:3px;\n";
|
|
|
781 print HTMLSNP " border-style:solid; \n";
|
|
|
782 print HTMLSNP " background-color : #c6c3bd; \n";
|
|
|
783 print HTMLSNP " }\n";
|
|
|
784
|
|
|
785 print HTMLSNP ".td2 { \n";
|
|
|
786 print HTMLSNP " border-color:black;\n";
|
|
|
787 print HTMLSNP " font-size: 11pt;\n";
|
|
|
788 print HTMLSNP " font-family: calibri;\n";
|
|
|
789 print HTMLSNP " border-width:1px;\n";
|
|
|
790 print HTMLSNP " border-left:3px;\n";
|
|
|
791 print HTMLSNP " border-right:3px;\n";
|
|
|
792 print HTMLSNP " border-style:solid; \n";
|
|
|
793 print HTMLSNP " background-color : #c6c3ee; \n";
|
|
|
794 print HTMLSNP " }\n";
|
|
|
795
|
|
|
796 print HTMLSNP ".ted { \n";
|
|
|
797 print HTMLSNP " border-color:black;\n";
|
|
|
798 print HTMLSNP " font-weight : bold;\n";
|
|
|
799 print HTMLSNP " background-color : #A19EED; \n";
|
|
|
800 print HTMLSNP " }\n";
|
|
|
801
|
|
|
802 print HTMLSNP ".ted2 { \n";
|
|
|
803 print HTMLSNP " border-color:black;\n";
|
|
|
804 print HTMLSNP " font-weight : bold;\n";
|
|
|
805 print HTMLSNP " background-color : #9A9D7C; \n";
|
|
|
806 print HTMLSNP " }\n";
|
|
|
807
|
|
|
808 print HTMLSNP ".tedG { \n";
|
|
|
809 print HTMLSNP " border-left:3px;\n";
|
|
|
810 print HTMLSNP " border-style:solid; \n";
|
|
|
811 print HTMLSNP " border-color:black;\n";
|
|
|
812 print HTMLSNP " font-weight : bold;\n";
|
|
|
813 print HTMLSNP " background-color : #A19EED; \n";
|
|
|
814 print HTMLSNP " }\n";
|
|
|
815
|
|
|
816 print HTMLSNP ".tedG2 { \n";
|
|
|
817 print HTMLSNP " border-left:3px;\n";
|
|
|
818 print HTMLSNP " border-style:solid; \n";
|
|
|
819 print HTMLSNP " border-color:black;\n";
|
|
|
820 print HTMLSNP " font-weight : bold;\n";
|
|
|
821 print HTMLSNP " background-color : #9A9D7C; \n";
|
|
|
822 print HTMLSNP " }\n";
|
|
|
823
|
|
|
824 print HTMLSNP ".final { \n";
|
|
|
825 print HTMLSNP " border-left:3px;\n";
|
|
|
826 print HTMLSNP " border-right:0px;\n";
|
|
|
827 print HTMLSNP " border-top:0px;\n";
|
|
|
828 print HTMLSNP " border-bottom:0px;\n";
|
|
|
829 print HTMLSNP " border-style:solid; \n";
|
|
|
830 print HTMLSNP " border-color:black;\n";
|
|
|
831 print HTMLSNP " background-color : white; \n";
|
|
|
832 print HTMLSNP " }\n";
|
|
|
833
|
|
|
834 print HTMLSNP ".auto-style1 {";
|
|
|
835 print HTMLSNP " font-weight: normal;";
|
|
|
836 print HTMLSNP " font-size: x-small;";
|
|
|
837 print HTMLSNP "}";
|
|
|
838
|
|
|
839
|
|
|
840 print HTMLSNP "</style>\n";
|
|
|
841
|
|
|
842 print HTMLCOUNT "<style type=\"text/css\">\n";
|
|
|
843
|
|
|
844 print HTMLCOUNT "th {\n";
|
|
|
845 print HTMLCOUNT " border-style:solid; \n";
|
|
|
846 print HTMLCOUNT " border-color:black;\n";
|
|
|
847 print HTMLCOUNT " border-width:3px;\n";
|
|
|
848 print HTMLCOUNT " font-family:calibri;\n";
|
|
|
849 print HTMLCOUNT " }\n";
|
|
|
850
|
|
|
851 print HTMLCOUNT "table {\n";
|
|
|
852 print HTMLCOUNT " margin:auto;\n";
|
|
|
853 print HTMLCOUNT " border-collapse: collapse;\n";
|
|
|
854 print HTMLCOUNT " border-width:3px; \n";
|
|
|
855 print HTMLCOUNT " border-style:solid; \n";
|
|
|
856 print HTMLCOUNT " border-color:black;\n";
|
|
|
857 print HTMLCOUNT " }\n";
|
|
|
858
|
|
|
859 print HTMLCOUNT ".th {\n";
|
|
|
860 print HTMLCOUNT " font-weight : normal;\n";
|
|
|
861 print HTMLCOUNT " border-style:solid; \n";
|
|
|
862 print HTMLCOUNT " border-color:white;\n";
|
|
|
863 print HTMLCOUNT " border-width:0px;\n";
|
|
|
864 print HTMLCOUNT " font-family:consolas;\n";
|
|
|
865 print HTMLCOUNT " }\n";
|
|
|
866
|
|
|
867 print HTMLCOUNT ".tab2 {\n";
|
|
|
868 print HTMLCOUNT " margin:auto;\n";
|
|
|
869 print HTMLCOUNT " border-collapse: collapse;\n";
|
|
|
870 print HTMLCOUNT " border-style:solid; \n";
|
|
|
871 print HTMLCOUNT " border-width:3px; \n";
|
|
|
872 print HTMLCOUNT " border-color:white;\n";
|
|
|
873 print HTMLCOUNT " }\n";
|
|
|
874
|
|
|
875 print HTMLCOUNT ".tab {\n";
|
|
|
876 print HTMLCOUNT " margin:auto;\n";
|
|
|
877 print HTMLCOUNT " border-collapse: collapse;\n";
|
|
|
878 print HTMLCOUNT " border-width:3px;\n ";
|
|
|
879 print HTMLCOUNT " border-style:solid;\n ";
|
|
|
880 print HTMLCOUNT " border-color:black;\n";
|
|
|
881 print HTMLCOUNT " }\n";
|
|
|
882
|
|
|
883 print HTMLCOUNT ".td1 { \n";
|
|
|
884 print HTMLCOUNT " border-color:black;\n";
|
|
|
885 print HTMLCOUNT " font-size: 11pt;\n";
|
|
|
886 print HTMLCOUNT " font-family: calibri;\n";
|
|
|
887 print HTMLCOUNT " border-width:1px;\n";
|
|
|
888 print HTMLCOUNT " border-left:3px;\n";
|
|
|
889 print HTMLCOUNT " border-right:3px;\n";
|
|
|
890 print HTMLCOUNT " border-style:solid; \n";
|
|
|
891 print HTMLCOUNT " background-color : #c6c3bd; \n";
|
|
|
892 print HTMLCOUNT " }\n";
|
|
|
893
|
|
|
894 print HTMLCOUNT ".td2 { \n";
|
|
|
895 print HTMLCOUNT " border-color:black;\n";
|
|
|
896 print HTMLCOUNT " font-size: 11pt;\n";
|
|
|
897 print HTMLCOUNT " font-family: calibri;\n";
|
|
|
898 print HTMLCOUNT " border-width:1px;\n";
|
|
|
899 print HTMLCOUNT " border-left:3px;\n";
|
|
|
900 print HTMLCOUNT " border-right:3px;\n";
|
|
|
901 print HTMLCOUNT " border-style:solid; \n";
|
|
|
902 print HTMLCOUNT " background-color : #c6c3ee; \n";
|
|
|
903 print HTMLCOUNT " }\n";
|
|
|
904
|
|
|
905 print HTMLCOUNT ".td3 { \n";
|
|
|
906 print HTMLCOUNT " border-color:black;\n";
|
|
|
907 print HTMLCOUNT " font-size: 11pt;\n";
|
|
|
908 print HTMLCOUNT " font-weight: bold;\n";
|
|
|
909 print HTMLCOUNT " font-family: calibri;\n";
|
|
|
910 print HTMLCOUNT " border-width:3px;\n";
|
|
|
911 print HTMLCOUNT " border-left:3px;\n";
|
|
|
912 print HTMLCOUNT " border-right:3px;\n";
|
|
|
913 print HTMLCOUNT " border-style:solid; \n";
|
|
|
914 print HTMLCOUNT " background-color : white; \n";
|
|
|
915 print HTMLCOUNT " }\n";
|
|
|
916
|
|
|
917
|
|
|
918 print HTMLCOUNT ".ted { \n";
|
|
|
919 print HTMLCOUNT " border-color:black;\n";
|
|
|
920 print HTMLCOUNT " font-weight : bold;\n";
|
|
|
921 print HTMLCOUNT " background-color : #A19EED; \n";
|
|
|
922 print HTMLCOUNT " }\n";
|
|
|
923
|
|
|
924 print HTMLCOUNT ".ted2 { \n";
|
|
|
925 print HTMLCOUNT " border-color:black;\n";
|
|
|
926 print HTMLCOUNT " font-weight : bold;\n";
|
|
|
927 print HTMLCOUNT " background-color : #9A9D7C; \n";
|
|
|
928 print HTMLCOUNT " }\n";
|
|
|
929
|
|
|
930 print HTMLCOUNT ".ted3 { \n";
|
|
|
931 print HTMLCOUNT " border-color:black;\n";
|
|
|
932 print HTMLCOUNT " font-family: calibri;\n";
|
|
|
933 print HTMLCOUNT " color: white;\n";
|
|
|
934 print HTMLCOUNT " background-color : #333333; \n";
|
|
|
935 print HTMLCOUNT " }\n";
|
|
|
936
|
|
|
937 print HTMLCOUNT ".auto-style1 {";
|
|
|
938 print HTMLCOUNT " font-weight: normal;";
|
|
|
939 print HTMLCOUNT " font-size: x-small;";
|
|
|
940 print HTMLCOUNT "}";
|
|
|
941
|
|
|
942 print HTMLCOUNT "</style>\n";
|
|
|
943
|
|
|
944 ###################################################################################################################################################################################
|
|
|
945
|
|
|
946 print HTMLSNP "</head>\n";
|
|
|
947
|
|
|
948 print HTMLSNP "<center><img src=\"".$REPimages."SNiPloid7.png\" WIDTH=250></center>";
|
|
|
949 if ($poly_poly_analysis == 0) {
|
|
|
950 print HTMLSNP "<center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center>";
|
|
|
951 }
|
|
|
952 print HTMLSNP "<p>\n";
|
|
|
953 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
|
|
954 print HTMLCOUNT "</head>\n";
|
|
|
955 print HTMLCOUNT "<table><tr><td class=\"tab2\"><img src=\"".$REPimages."SNiPloid7.png\" WIDTH=250>";
|
|
|
956
|
|
|
957 print HTMLCOUNT "<h3><font face=\"calibri\">Synthesis of the analysis</font></h3></td>";
|
|
|
958 if ($poly_poly_analysis == 0) {
|
|
|
959
|
|
|
960 print HTMLCOUNT "<td class=\"tab2\" width=50></td>";
|
|
|
961 print HTMLCOUNT "<td class=\"tab2\"><table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\">";
|
|
|
962 print HTMLCOUNT "<tr><th>Diploids</th><th>Polyploid</th><th>Identity</th><th>Interpretation</th></tr>";
|
|
|
963 print HTMLCOUNT "<tr><td>[1/2]</td><td>[1]</td><td>!=</td><td><img src=\"".$REPimages."1.png\" height=30></td></tr>";
|
|
|
964 print HTMLCOUNT "<tr><td>[1/2]</td><td>[2]</td><td>!=</td><td><img src=\"".$REPimages."2.png\" height=30></td></tr>";
|
|
|
965 print HTMLCOUNT "<tr><td>[1]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."3.png\" height=30></td></tr>";
|
|
|
966 print HTMLCOUNT "<tr><td>[2]</td><td>[1/2]</td><td>!=</td><td><img src=\"".$REPimages."4.png\" height=30></td></tr>";
|
|
|
967 print HTMLCOUNT "<tr><td>[1/2]</td><td>[1/2]</td><td>=</td><td><img src=\"".$REPimages."5v.png\" height=30></td></tr>";
|
|
|
968 print HTMLCOUNT "<tr><td>[1]</td><td>[2]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>";
|
|
|
969 print HTMLCOUNT "<tr><td>[1]</td><td>[2/3]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>";
|
|
|
970 print HTMLCOUNT "<tr><td>[1/2]</td><td>[2/3]</td><td>!=</td><td><img src=\"".$REPimages."other.png\" height=30></td></tr>";
|
|
|
971 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>";
|
|
|
972 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>";
|
|
|
973 print HTMLCOUNT "</table></td>";
|
|
|
974 print HTMLCOUNT "<td class=\"tab2\" width=50></td>";
|
|
|
975 print HTMLCOUNT "<td class=\"tab2\"><center><img src=\"".$REPimages."arbre.png\" WIDTH=400></center></td>";
|
|
|
976 #print HTMLCOUNT "<td><table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"><tr><th>Diploids</th><th>Polyploid</th><th>Identity</th><th>Interpretation</th></tr></table></td>";
|
|
|
977 print HTMLCOUNT "</tr></table>";
|
|
|
978 }
|
|
|
979 print HTMLCOUNT "<p>\n";
|
|
|
980 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
|
|
981
|
|
|
982 print HTMLSNP "<body>\n";
|
|
|
983
|
|
|
984 if ($poly_poly_analysis == 1) {
|
|
|
985 print HTMLSNP "<center><h3><font face=\"calibri\">Result of SNP comparison of two Polyploids</font></h3></center>";
|
|
|
986 }
|
|
|
987 else {
|
|
|
988 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>";
|
|
|
989 }
|
|
|
990
|
|
|
991 print HTMLSNP "<p>\n";
|
|
|
992
|
|
|
993 # COLUMNS - HTMLSNP SNP VIEW
|
|
|
994 print HTMLSNP "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n";
|
|
|
995 print HTMLSNP "<tr>\n";
|
|
|
996 print HTMLSNP "<th>Gene</th>"; # (1) Gene
|
|
|
997 print HTMLSNP "<th>Position</th>"; # (2) Position
|
|
|
998
|
|
|
999 if ($poly_poly_analysis == 1) {
|
|
|
1000 print HTMLSNP "<th>REF<br></th>";
|
|
|
1001 print HTMLSNP "<th>Polyploid 1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (3) Polyploid
|
|
|
1002 print HTMLSNP "<th>Polyploid 2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (4) Polyploid 2
|
|
|
1003
|
|
|
1004 print HTMLSNP "<th>[Filtered/Total] Depth<br>Polyploid 1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (8) Filtered Depth
|
|
|
1005 print HTMLSNP "<th>[Filtered/Total] Depth<br>Polyploid 2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (9) Total Depth
|
|
|
1006
|
|
|
1007 # Entête fichier SNP VIEW TAB
|
|
|
1008 print TABSNP "Gene\t"; # (1) Gene
|
|
|
1009 print TABSNP "Position\t"; # (2) Position
|
|
|
1010 print TABSNP "REF\t"; # (2) Position
|
|
|
1011 print TABSNP "Polyploid 1: ".$polyploidName."\t"; # (3) Polyploid
|
|
|
1012 print TABSNP "Polyploid 2: ".$genome1Name."\t"; # (4) Genome 1
|
|
|
1013 print TABSNP "P1 Filtered Depth\t"; # (9) Filtered Depth
|
|
|
1014 print TABSNP "P1 Total Depth\t"; # (10) Total Depth
|
|
|
1015 print TABSNP "P2 Filtered Depth\t"; # (9) Filtered Depth
|
|
|
1016 print TABSNP "P2 Total Depth\n"; # (10) Total Depth
|
|
|
1017 }
|
|
|
1018 else {
|
|
|
1019 # (3) Reference
|
|
|
1020 print HTMLSNP "<th>Polyploid<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (3) Polyploid
|
|
|
1021 print HTMLSNP "<th>Genome 1<br><span class=\"auto-style1\">".$genome1Name."</span></th>"; # (4) Genome 1
|
|
|
1022 print HTMLSNP "<th>Genome 2<br><span class=\"auto-style1\">".$genome2Name."</span></th>"; # (5) Genome 2
|
|
|
1023 print HTMLSNP "<th>Validation</th>";
|
|
|
1024 print HTMLSNP "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>"; # (7) Ratio
|
|
|
1025 print HTMLSNP "<th>Filtered<br>Depth</th>"; # (8) Filtered Depth
|
|
|
1026 print HTMLSNP "<th>Total<br>Depth</th>"; # (9) Total Depth
|
|
|
1027 print HTMLSNP "<th>SNP Class</th>"; # (9) Total Depth
|
|
|
1028
|
|
|
1029 # Entête fichier SNP VIEW TAB
|
|
|
1030 print TABSNP "Gene\t"; # (1) Gene
|
|
|
1031 print TABSNP "Position\t"; # (2) Position
|
|
|
1032 print TABSNP "Polyploid: ".$polyploidName."\t"; # (3) Polyploid
|
|
|
1033 print TABSNP "Genome 1: ".$genome1Name."\t"; # (4) Genome 1
|
|
|
1034 print TABSNP "Genome 2: ".$genome2Name."\t"; # (5) Genome 2
|
|
|
1035 print TABSNP "Validation\t"; # (6) Validation
|
|
|
1036 print TABSNP "Ratio (%) ".$genome2Name."\t"; # (7) Ratio Genome 1
|
|
|
1037 print TABSNP "Ratio (%) ".$genome1Name."\t"; # (8) Ratio Genome 2
|
|
|
1038 print TABSNP "Filtered Depth\t"; # (9) Filtered Depth
|
|
|
1039 print TABSNP "Total Depth\t"; # (10) Total Depth
|
|
|
1040 print TABSNP "SNP Class\n"; # (10) Total Depth
|
|
|
1041 }
|
|
|
1042 print HTMLSNP "</tr>\n";
|
|
|
1043
|
|
|
1044
|
|
|
1045
|
|
|
1046 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
|
|
1047 print HTMLCOUNT "<body>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n";
|
|
|
1048 print HTMLCOUNT "<p>\n";
|
|
|
1049 # COLUMNS - HTML SYNTHESIS
|
|
|
1050 print HTMLCOUNT "<table border=\"1\" border cellpadding=\"5\" style=\"text-align:center;\"> \n";
|
|
|
1051 print HTMLCOUNT "<tr>\n";
|
|
|
1052 print HTMLCOUNT "<th>Gene</th>"; # (1) Gene
|
|
|
1053 print HTMLCOUNT "<th>Interval Size<br>Analysed (pb)</th>"; # (2) Interval Size Analyzed
|
|
|
1054 print HTMLCOUNT "<th>nb Positions<br>with SNP</th>";
|
|
|
1055 if ($poly_poly_analysis == 0) { # (3) nB Positions With SNP
|
|
|
1056 print HTMLCOUNT "<th><img src=\"".$REPimages."1.png\" height=30></th>"; # (4) [1]
|
|
|
1057 print HTMLCOUNT "<th><img src=\"".$REPimages."2.png\" height=30></th>"; # (5) [2]
|
|
|
1058 print HTMLCOUNT "<th><img src=\"".$REPimages."3ou4.png\" height=30></th>"; # (6) [3 or 4]
|
|
|
1059 print HTMLCOUNT "<th><img src=\"".$REPimages."3.png\" height=30></th>"; # (6) [3 or 4]
|
|
|
1060 print HTMLCOUNT "<th><img src=\"".$REPimages."4.png\" height=30></th>"; # (6) [3 or 4]
|
|
|
1061 print HTMLCOUNT "<th><img src=\"".$REPimages."5v.png\" height=30></th>"; # (11) [5]
|
|
|
1062 print HTMLCOUNT "<th><img src=\"".$REPimages."other.png\" height=30></th>"; # (7) [other]
|
|
|
1063 print HTMLCOUNT "<th><img src=\"".$REPimages."HG1.png\" height=30><br><span class=\"auto-style1\">".$genome1Name."</span></th>"; # (8) Heterozygosity For Genome 1
|
|
|
1064 print HTMLCOUNT "<th>SNP Intra-Diploids <br><img src=\"".$REPimages."5v.png\" height=30> + <img src=\"".$REPimages."1.png\" height=30> + <img src=\"".$REPimages."2.png\" height=30> + <img src=\"".$REPimages."other.png\" height=30></th>"; # (9) SNP Diploids
|
|
|
1065 print HTMLCOUNT "<th>SNP Intra-Polyploid <br> <img src=\"".$REPimages."5v.png\" height=30> + <img src=\"".$REPimages."3ou4.png\" height=30> + <img src=\"".$REPimages."other.png\" height=30></th>"; # (10) SNP Polyploid
|
|
|
1066 print HTMLCOUNT "<th>Ratio (%)<br><span class=\"auto-style1\">".$genome2Name." : ".$genome1Name."</span></th>\n\n\n\n\n\n\n\n"; # (12) Ratio %
|
|
|
1067
|
|
|
1068 print HTMLCOUNT "</tr>\n";
|
|
|
1069 # Entête HTMLSNP Synthesis
|
|
|
1070 print TABCOUNT "Gene\t"; # (1) Gene
|
|
|
1071 print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb)
|
|
|
1072 print TABCOUNT "nb SNP positions\t"; # (3) nb SNP positions
|
|
|
1073 print TABCOUNT "1\t"; # (4) [1]
|
|
|
1074 print TABCOUNT "2\t"; # (5) [2]
|
|
|
1075 print TABCOUNT "3 or 4\t"; # (6) [3 or 4]
|
|
|
1076 print TABCOUNT "3\t"; # (6) [3 or 4]
|
|
|
1077 print TABCOUNT "4\t"; # (6) [3 or 4]
|
|
|
1078 print TABCOUNT "5\t"; # (11) [5]
|
|
|
1079 print TABCOUNT "other\t"; # (7) [other]
|
|
|
1080 print TABCOUNT "SNP Heterozygosity Genome 1\t"; # (8) SNP Heterozygosity Genome 1
|
|
|
1081 print TABCOUNT "SNP Diploids\t"; # (9) SNP Diploids
|
|
|
1082 print TABCOUNT "SNP Polyploid\t"; # (10) SNP Polyploid
|
|
|
1083 print TABCOUNT "Ratio (%) ".$genome2Name."\t"; # (12) Ratio (%) Genome 2
|
|
|
1084 print TABCOUNT "Ratio (%) ".$genome1Name."\n"; # (13) Ratio (%) Genome 1
|
|
|
1085 }
|
|
|
1086 else {
|
|
|
1087 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]
|
|
|
1088 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]
|
|
|
1089 print HTMLCOUNT "<th>SNP<br>interpolyploids<br>P1 ≠ P2<br><span style=\"auto-style1\"></span></th>"; # (4) [1] #DE8A8A
|
|
|
1090 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]
|
|
|
1091 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]
|
|
|
1092 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]
|
|
|
1093 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]
|
|
|
1094 print HTMLCOUNT "<th>SNP<br>intra P1<br><span class=\"auto-style1\">".$polyploidName."</span></th>"; # (4) [1]
|
|
|
1095 print HTMLCOUNT "<th>SNP<br>intra P2<br><span class=\"auto-style1\">".$polyploid2Name."</span></th>"; # (4) [1]
|
|
|
1096
|
|
|
1097 print HTMLCOUNT "</tr>\n";
|
|
|
1098 # Entête HTMLSNP Synthesis
|
|
|
1099 print TABCOUNT "Gene\t"; # (1) Gene
|
|
|
1100 print TABCOUNT "Interval Size Analysed (pb)\t"; # (2) Interval Size Analysed (pb)
|
|
|
1101 print TABCOUNT "nb positions with SNP\t"; # (3) nb SNP positions
|
|
|
1102 print TABCOUNT "P1 = P2 [1/2] vs [1/2]\t"; # (4) [1]
|
|
|
1103 print TABCOUNT "P1 = P2 [1] vs [1]\t"; # (4) [1]
|
|
|
1104 print TABCOUNT "SNP interpolyploids P1 diff P2\t"; # (4) [1] #DE8A8A
|
|
|
1105 print TABCOUNT "P1 diff P2 2 Alleles [1] vs [2]\t"; # (4) [1]
|
|
|
1106 print TABCOUNT "P1 diff P2 2 Alleles [1/2] vs [1] or [2]\t"; # (4) [1]
|
|
|
1107 print TABCOUNT "P1 diff P2 3 Alleles [1/2] vs [3]\t"; # (4) [1]
|
|
|
1108 print TABCOUNT "P1 diff P2 3 Alleles [1/2] vs [1/3]\t"; # (4) [1]
|
|
|
1109 print TABCOUNT "SNP intra P1 ".$polyploidName."\t" ; # (4) [1]
|
|
|
1110 print TABCOUNT "SNP intra P2 ".$polyploid2Name."\n" ; # (4) [1]
|
|
|
1111
|
|
|
1112 }
|
|
|
1113 #----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
|
|
|
1114 $ligneInter = 0 ;
|
|
|
1115 $totalSNP = 0 ;
|
|
|
1116 $totalSize = 0 ;
|
|
|
1117
|
|
|
1118 $total11 = 0 ;
|
|
|
1119 $total22 = 0 ;
|
|
|
1120 $total3ou4 = 0 ;
|
|
|
1121 $total5 = 0 ;
|
|
|
1122 $total512 = 0 ;
|
|
|
1123 $total534 = 0 ;
|
|
|
1124 $totalOther = 0 ;
|
|
|
1125 $totalGenome2 = 0 ;
|
|
|
1126
|
|
|
1127 $total3 = 0 ;
|
|
|
1128 $total4 = 0 ;
|
|
|
1129
|
|
|
1130 $totalNbPolyploid1 = 0 ; # SNP heterozygosity for P1
|
|
|
1131 $totalNbPolyploid2 = 0 ; # SNP heterozygosity for P2
|
|
|
1132 $totalNbCommuns = 0 ; # SNP heterozygosity [P1] = [P2]
|
|
|
1133 $totalNbCommunsHomo = 0 ; # SNP homozygosity [P1] = [P2]
|
|
|
1134 $totalNbDifferent = 0 ; # [P1] ne [P2]
|
|
|
1135 $totalNbHomoDiff = 0 ; # Example : P1 = [A] ; P2 = [G]
|
|
|
1136 $totalNbAlleleCommun = 0 ; # Example : P1 = [A/G] ; P2 = [A]
|
|
|
1137 $totalAlleleDifferent = 0 ; # Example : P1 = [A/G] ; P2 = [C] or [T]
|
|
|
1138 $totalAlleleCommunH = 0 ; # Example : P1 = [A/G] ; P2 = [A/C]
|
|
|
1139
|
|
|
1140 }
|
|
|
1141
|
|
|
1142 sub int_output { # intern reference
|
|
|
1143
|
|
|
1144 foreach my $s(sort(keys(%snp_final))){
|
|
|
1145 #######################################
|
|
|
1146 if ($ligneInter == 0) {
|
|
|
1147 print HTMLSNP "<tr class=\"bord1\">\n";
|
|
|
1148 print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n";
|
|
|
1149 }
|
|
|
1150 else {
|
|
|
1151 print HTMLSNP "<tr class=\"bord2\">\n";
|
|
|
1152 print HTMLCOUNT "<tr class=\"td2\">\n";
|
|
|
1153 }
|
|
|
1154 #######################################
|
|
|
1155
|
|
|
1156 my $ref = $snp_final{$s};
|
|
|
1157 my %hash = %$ref;
|
|
|
1158 $taille = keys(%hash);
|
|
|
1159
|
|
|
1160 # taille de la ligne gene
|
|
|
1161 print HTMLSNP "<td rowspan=\"".$taille."\"><b>".$s."</b></td>";
|
|
|
1162
|
|
|
1163 $ligneOK = 0 ;
|
|
|
1164
|
|
|
1165 $nbPolyploid = 0;
|
|
|
1166 $nbGenomes = 0 ;
|
|
|
1167 $nbGenome2 = 0 ; # SNP chez les diploides dans un cas "Other" avec genome 1 heterozygote
|
|
|
1168 $nbCommuns = 0;
|
|
|
1169 $nbPoly_only = 0 ;
|
|
|
1170 $nbSub_only = 0 ;
|
|
|
1171
|
|
|
1172 $case5 = 0 ;
|
|
|
1173 $case1 = 0 ;
|
|
|
1174 $case2 = 0 ;
|
|
|
1175 $case3ou4 = 0;
|
|
|
1176 $case3 = 0 ;
|
|
|
1177 $case4 = 0 ;
|
|
|
1178 $caseOther = 0;
|
|
|
1179 $casePolyplother = 0 ; # SNP chez le polyploide dans un cas "Other"
|
|
|
1180 $caseDiplother = 0 ; # SNP chez les diploides dans un cas "Other"
|
|
|
1181
|
|
|
1182
|
|
|
1183
|
|
|
1184 # Moyenne Ponderee
|
|
|
1185 $moyenneSNPindep1 = 0 ;
|
|
|
1186 $moyenneSNPindep2 = 0 ;
|
|
|
1187
|
|
|
1188 @tabTrie = sort ({ $a <=> $b }keys %hash);
|
|
|
1189
|
|
|
1190 #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) {
|
|
|
1191 foreach my $c(@tabTrie) {
|
|
|
1192 if ($ligneOK == 1) {
|
|
|
1193 if ($ligneInter == 0) {
|
|
|
1194 print HTMLSNP "<tr class=\"td1\">\n";
|
|
|
1195 }
|
|
|
1196 else {
|
|
|
1197 print HTMLSNP "<tr class=\"td2\">\n";
|
|
|
1198 }
|
|
|
1199 }
|
|
|
1200 ################################################################################
|
|
|
1201 ### Recuperation des informations ###
|
|
|
1202
|
|
|
1203 ($code_snp,$ratio,$GT_poly,$DP_P,$code_G1,$GT_G1) = split(/\t/,$snp_final{$s}{$c});
|
|
|
1204 ($DP_P, $FDP) = split(/-/, $DP_P);
|
|
|
1205 #print STDOUT "\n($code_snp:$GT_poly) - ($code_G1:$GT_G1)" ;
|
|
|
1206 if ($GT_poly ne "") { # Polyploide = [0.0] ou [0.1] ou [1.1]
|
|
|
1207 @recupAlleles = split(/\[/,$code_snp);
|
|
|
1208 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
1209 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
|
|
|
1210 # Attribution des alleles au polyploide si pas de SNP
|
|
|
1211 if ($GT_poly =~ /^0.0$/) { $code_snp = $alRef ; }
|
|
|
1212 if ($GT_poly =~ /^1.1$/) { $code_snp = $alAltP ; }
|
|
|
1213 # Attribution des alleles au genome 1 si pas de SNP
|
|
|
1214 if (($GT_G1 eq "") || ($GT_G1 =~ /^0.0$/)) { $code_G1 = $alRef ; }
|
|
|
1215 if ($GT_G1 =~ /^1.1$/) {
|
|
|
1216 @recupAlleles = split(/\[/,$code_G1);
|
|
|
1217 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
1218 ($alRef,$alAlt) = split(/\//,$recupAlleles[0]);
|
|
|
1219 $code_G1 = $alAlt;
|
|
|
1220 }
|
|
|
1221 }
|
|
|
1222 elsif ($GT_G1 ne "") { # pas de SNP polyploide dans le fichier 1 (fichiers non mergés) -> equivalent de [0.0]
|
|
|
1223 @recupAlleles = split(/\[/,$code_G1);
|
|
|
1224 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
1225 ($alRef,$alAlt) = split(/\//,$recupAlleles[0]);
|
|
|
1226 # Attribution des Alleles au genome 1
|
|
|
1227 if ($GT_G1 =~ /^1.1$/) { $code_G1 = $alAlt ; }
|
|
|
1228 if ($GT_G1 =~ /^0.0$/) { $code_G1 = $alRef ; }
|
|
|
1229 }
|
|
|
1230
|
|
|
1231 ################################################################################
|
|
|
1232 $noSNPpoly = "ok" ;
|
|
|
1233
|
|
|
1234
|
|
|
1235
|
|
|
1236
|
|
|
1237 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_G1 =~ /^1.1$/)) && ($code_G1 eq $alAltP)) {
|
|
|
1238 if ($ligneInter == 0) {
|
|
|
1239 print HTMLSNP "<td class=\"tedG2\">".$c."</td>";
|
|
|
1240 print HTMLSNP "<td class=\"ted2\">".$code_snp."</td>";
|
|
|
1241 print HTMLSNP "<td class=\"ted2\">".$code_G1."</td>";
|
|
|
1242 print HTMLSNP "<td class=\"ted2\">".$alRef."</td>"; #REF
|
|
|
1243 print HTMLSNP "<td class=\"ted2\">OK</td>";
|
|
|
1244
|
|
|
1245 }
|
|
|
1246 else {
|
|
|
1247 print HTMLSNP "<td class=\"tedG\">".$c."</td>";
|
|
|
1248 print HTMLSNP "<td class=\"ted\">".$code_snp."</td>";
|
|
|
1249 print HTMLSNP "<td class=\"ted\">".$code_G1."</td>";
|
|
|
1250 print HTMLSNP "<td class=\"ted\">".$alRef."</td>"; #REF
|
|
|
1251 print HTMLSNP "<td class=\"ted\">OK</td>";
|
|
|
1252 }
|
|
|
1253 }
|
|
|
1254 else {
|
|
|
1255 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
1256 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
1257 print HTMLSNP "<td>".$code_G1."</td>";
|
|
|
1258 print HTMLSNP "<td>".$alRef."</td>"; #REF
|
|
|
1259 print HTMLSNP "<td>not OK</td>";
|
|
|
1260 }
|
|
|
1261 print TABSNP $s."\t".$c."\t".$code_snp."\t".$code_G1."\t".$alRef."\t";
|
|
|
1262
|
|
|
1263
|
|
|
1264
|
|
|
1265 $tailleImg = 35 ;
|
|
|
1266
|
|
|
1267
|
|
|
1268 if (($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) { # SNP POLYPLOID - [0/1] [0|1] [1|0]
|
|
|
1269 # Moyenne du Ratio -----------------------------------
|
|
|
1270 ($sub1,$sub2) = split(",",$ratio);
|
|
|
1271 $somme = $sub1 + $sub2 ;
|
|
|
1272
|
|
|
1273 if ($somme == 0 ) {
|
|
|
1274 print STDOUT "ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"";
|
|
|
1275 die ("ERROR : Cannot calculate ratio for ".$gene." [pos:".$position."]\n\"".$line."\"");
|
|
|
1276 }
|
|
|
1277 else {
|
|
|
1278 $ratio = ($sub1/($sub1+$sub2))*100;
|
|
|
1279 $ratio = sprintf("%.0f", $ratio);
|
|
|
1280 }
|
|
|
1281 #$ratio = sprintf("%.0f", $ratio);
|
|
|
1282 $ratio2 = 100-$ratio ;
|
|
|
1283
|
|
|
1284 #-----------------------------------------------------
|
|
|
1285 if (($GT_G1 =~ /^1.1$/)){ # Pas de SNP Genome1 [1/1] [1|1] SNP entre genome1 et genome2
|
|
|
1286 if ($code_G1 eq $alAltP) { # 5
|
|
|
1287 $moyenneSNPindep1 = $moyenneSNPindep1 + $ratio ;
|
|
|
1288 $moyenneSNPindep2 = $moyenneSNPindep2 + $ratio2 ;
|
|
|
1289 if ($ligneInter == 0) {
|
|
|
1290 print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO %
|
|
|
1291 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
|
|
|
1292 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2
|
|
|
1293 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>";
|
|
|
1294 print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>";
|
|
|
1295 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=".$tailleImg."></td>";
|
|
|
1296
|
|
|
1297 }
|
|
|
1298 else {
|
|
|
1299 print HTMLSNP "<td class=\"ted\">".$ratio.":".$ratio2."<br>"; # RATIO %
|
|
|
1300 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
|
|
|
1301 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2.">"; # IMG RATIO 2
|
|
|
1302 print HTMLSNP "<td class=\"ted\">".$FDP."</td>";
|
|
|
1303 print HTMLSNP "<td class=\"ted\">".$DP_P."</td>";
|
|
|
1304 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=".$tailleImg."></td>";
|
|
|
1305
|
|
|
1306 }
|
|
|
1307 print TABSNP "OK\t".$ratio."\t".$ratio2."\t".$FDP."\t".$DP_P."\t5";
|
|
|
1308 $case5 ++ ;
|
|
|
1309 }
|
|
|
1310 else { # Other 0.1 - 1.1 (O GA A) # Other [SNP DIPLO + SNP POLY]
|
|
|
1311 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1312 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
|
|
|
1313 print TABSNP "not OK\t#\t#\t#\t#\tother";
|
|
|
1314 $caseOther ++ ;
|
|
|
1315 $casePolyplother ++ ;
|
|
|
1316 $caseDiplother ++ ;
|
|
|
1317 }
|
|
|
1318 }
|
|
|
1319 else {
|
|
|
1320 if (($GT_G1 =~ /^0.0$/)||($GT_G1 =~ /^$/)){ # 3 ou 4
|
|
|
1321
|
|
|
1322 ###############################################################################################
|
|
|
1323 # PHASING
|
|
|
1324 ###############################################################################################
|
|
|
1325 $phasedornot = 0 ;
|
|
|
1326 my $is_3 = 0;
|
|
|
1327 my $is_4 = 0;
|
|
|
1328 if ($GT_poly =~/\|/){
|
|
|
1329
|
|
|
1330 #print STDOUT $s."\n";
|
|
|
1331 my $ref = $phased_regions{$s};
|
|
|
1332 my %hash = %$ref ;
|
|
|
1333 foreach my $num_reg(sort(keys(%hash))){
|
|
|
1334 if (exists $phased_regions{$s}{$num_reg}{$c}) {
|
|
|
1335 $genotype = $phased_regions{$s}{$num_reg}{$c} ;
|
|
|
1336 my $ref2 = $phased_regions{$s}{$num_reg};
|
|
|
1337 my %hash2 = %$ref2 ;
|
|
|
1338 foreach my $pos(sort(keys(%hash2))){
|
|
|
1339 if (exists $five{$s}{$pos}){
|
|
|
1340 if (($five{$s}{$pos} =~ /0.1/ && $GT_poly =~ /0.1/) or ($five{$s}{$pos} =~ /1.0/ && $GT_poly =~ /1.0/)){
|
|
|
1341 print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO %
|
|
|
1342 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
|
|
|
1343 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2
|
|
|
1344 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>";
|
|
|
1345 print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>";
|
|
|
1346 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3.png\" height=".$tailleImg."></td>";
|
|
|
1347 $case3 ++ ;
|
|
|
1348 $is_3 = 1;
|
|
|
1349 }
|
|
|
1350 else {
|
|
|
1351 print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO %
|
|
|
1352 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
|
|
|
1353 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2
|
|
|
1354 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>";
|
|
|
1355 print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>";
|
|
|
1356
|
|
|
1357 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."4.png\" height=".$tailleImg."></td>";
|
|
|
1358 $case4 ++ ;
|
|
|
1359 $is_4 = 1;
|
|
|
1360 }
|
|
|
1361 $phasedornot = 1 ;
|
|
|
1362 last ;
|
|
|
1363 }
|
|
|
1364 }
|
|
|
1365 }
|
|
|
1366 }
|
|
|
1367 #print STDOUT "\n";
|
|
|
1368 }
|
|
|
1369 if ($phasedornot == 0) {
|
|
|
1370 print HTMLSNP "<td class=\"ted2\">".$ratio.":".$ratio2."<br>"; # RATIO %
|
|
|
1371 print HTMLSNP "<img src=\"".$REPimages."r1.png\" height=10 width=".$ratio.">"; # IMG RATIO 1
|
|
|
1372 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=10 width=".$ratio2."></td>"; # IMG RATIO 2
|
|
|
1373 print HTMLSNP "<td class=\"ted2\">".$FDP."</td>";
|
|
|
1374 print HTMLSNP "<td class=\"ted2\">".$DP_P."</td>";
|
|
|
1375 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=".$tailleImg."></td>";
|
|
|
1376 $case3ou4 ++ ;
|
|
|
1377 }
|
|
|
1378
|
|
|
1379 ###############################################################################################
|
|
|
1380
|
|
|
1381
|
|
|
1382
|
|
|
1383 print TABSNP "not OK\t".$ratio."\t".$ratio2."\t".$FDP."\t".$DP_P."\t";
|
|
|
1384 if ($is_3){print TABSNP "3";}
|
|
|
1385 elsif ($is_4){print TABSNP "4";}
|
|
|
1386 else{print TABSNP "3or4";}
|
|
|
1387
|
|
|
1388 }
|
|
|
1389 else { #0/1
|
|
|
1390 # heterozygosity G1
|
|
|
1391 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1392 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>";
|
|
|
1393 print TABSNP "not OK\t#\t#\t#\t#\tother,heterozygosity for genome 1";
|
|
|
1394 $nbGenome2 ++ ;
|
|
|
1395 $casePolyplother ++ ;
|
|
|
1396 $caseOther ++ ;
|
|
|
1397 }
|
|
|
1398 }
|
|
|
1399 }
|
|
|
1400
|
|
|
1401 if (($GT_poly =~ /^1.1$/)) { # POLYPLOID NE REFERENCE - [1/1]
|
|
|
1402 if ($GT_G1 && ($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0]
|
|
|
1403 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1404 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>";
|
|
|
1405 print TABSNP "not OK\t#\t#\t#\t#\tother,heterozygosity for genome 1";
|
|
|
1406 $nbGenome2 ++ ;
|
|
|
1407 $caseOther ++ ;
|
|
|
1408 }
|
|
|
1409 elsif (!$GT_G1){ # POLYPLOID A/A DIPLOIDS T/T
|
|
|
1410 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1411 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
|
|
|
1412 print TABSNP "not OK\t#\t#\t#\t#\tother";
|
|
|
1413 $caseOther ++ ;
|
|
|
1414 }
|
|
|
1415
|
|
|
1416 else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2
|
|
|
1417 if ($GT_G1 =~ /^0.0$/){ # Other [NOTHING]
|
|
|
1418 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1419 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
|
|
|
1420 print TABSNP "not OK\t#\t#\t#\t#\tother";
|
|
|
1421 $caseOther ++ ;
|
|
|
1422 }
|
|
|
1423 else {
|
|
|
1424 if ($code_G1 eq $alAltP) { # 2
|
|
|
1425 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1426 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=".$tailleImg."></td>";
|
|
|
1427 print TABSNP "not OK\t#\t#\t#\t#\t2";
|
|
|
1428 $case2 ++ ;
|
|
|
1429 }
|
|
|
1430 else { # Other [SNP DIPLO]
|
|
|
1431 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1432 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."></td>";
|
|
|
1433 print TABSNP "not OK\t#\t#\t#\t#\tother";
|
|
|
1434 $caseOther ++ ;
|
|
|
1435 $caseDiplother ++ ;
|
|
|
1436 }
|
|
|
1437 }
|
|
|
1438 }
|
|
|
1439 }
|
|
|
1440
|
|
|
1441 if (($GT_poly =~ /^0.0$/)||($GT_poly =~ /^$/)) { #POLYPLOID == REFERENCE - [0|0]
|
|
|
1442 ####################################
|
|
|
1443 if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # SNP Genome1 intra [0/1] [0|1] [1|0]
|
|
|
1444 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1445 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=".$tailleImg."><img src=\"".$REPimages."HG1.png\" height=".$tailleImg."></td>";
|
|
|
1446 print TABSNP "not OK\t#\t#\t#\t#\tother,heterozygosity for genome 1";
|
|
|
1447 $nbGenome2 ++ ;
|
|
|
1448 $caseOther++;
|
|
|
1449 }
|
|
|
1450 else { # Pas de SNP Genome1 [0/0] [0|0] [1/1] [1|1] SNP entre genome1 et genome2
|
|
|
1451 if ($GT_G1 =~ /^1.1$/){
|
|
|
1452 print HTMLSNP "<td>#</td><td>#</td><td>#</td>";
|
|
|
1453 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=".$tailleImg."></td>";
|
|
|
1454 print TABSNP "not OK\t#\t#\t#\t#\t1";
|
|
|
1455 $case1 ++ ;
|
|
|
1456 }
|
|
|
1457 }
|
|
|
1458 }
|
|
|
1459
|
|
|
1460 print TABSNP "\n";
|
|
|
1461 print HTMLSNP "</tr>\n";
|
|
|
1462 $ligneOK = 1 ;
|
|
|
1463 }
|
|
|
1464
|
|
|
1465 if ($ligneInter == 0) {
|
|
|
1466 print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">".$s."</td>";
|
|
|
1467 }
|
|
|
1468 else {
|
|
|
1469 print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">".$s."</td>";
|
|
|
1470 }
|
|
|
1471 print TABCOUNT $s."\t";
|
|
|
1472
|
|
|
1473 #######################################
|
|
|
1474 if ($ligneInter == 0) { $ligneInter = 1 ; }
|
|
|
1475 else { $ligneInter = 0 ; }
|
|
|
1476 #######################################
|
|
|
1477
|
|
|
1478 # Calcul des intervalles #
|
|
|
1479 ##########################
|
|
|
1480 $taille_totale = 0 ;
|
|
|
1481 my $ref = $intervalle2{$s};
|
|
|
1482 my %hash = %$ref;
|
|
|
1483
|
|
|
1484 foreach my $interval(keys(%hash)){
|
|
|
1485 my @pos = split(/-/,$interval);
|
|
|
1486 $taille_inter = $pos[1]-$pos[0]+1 ;
|
|
|
1487 $taille_totale = $taille_totale + $taille_inter;
|
|
|
1488 }
|
|
|
1489 $total1 = $case5 + $case1 + $case2 + $caseDiplother + $nbGenome2;
|
|
|
1490 $total2 = $case5 + $case3ou4 + $casePolyplother;
|
|
|
1491
|
|
|
1492
|
|
|
1493
|
|
|
1494 # SYNTHESIS
|
|
|
1495 print HTMLCOUNT "<td>".$taille_totale."</td><td style=\"border-left:3px solid black\">".$taille."</td></td>";
|
|
|
1496 print HTMLCOUNT "<td style=\"border-left:3px solid black\">";
|
|
|
1497 print HTMLCOUNT $case1."</td><td>".$case2."</td><td>".$case3ou4."</td><td>";
|
|
|
1498 print HTMLCOUNT $case3."</td><td>".$case4."</td><td>".$case5."</td><td>";
|
|
|
1499 print HTMLCOUNT $caseOther."</td><td style=\"border-left:3px solid black\">".$nbGenome2."</td><td style=\"border-left:3px solid black\">".$total1."</td>";
|
|
|
1500 print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$total2."</td>";
|
|
|
1501 print TABCOUNT $taille_totale."\t".$taille."\t";
|
|
|
1502 print TABCOUNT $case1."\t".$case2."\t".$case3ou4."\t".$case3."\t".$case4."\t".$case5."\t".$caseOther."\t".$nbGenome2."\t".$total1."\t".$total2."\t";
|
|
|
1503
|
|
|
1504 $nbTotGenesAna ++ ;
|
|
|
1505
|
|
|
1506 if ($case5 != 0) {
|
|
|
1507 $nbTotGenesVal ++ ;
|
|
|
1508 if ($ligneInter == 1) {
|
|
|
1509 print HTMLCOUNT "<td class=\"ted2\" style=\"border-left:3px solid black\">";
|
|
|
1510 print HTMLCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."<br>";
|
|
|
1511 print HTMLCOUNT "<img src=\"".$REPimages."r1.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep1/$case5).">";
|
|
|
1512 print HTMLCOUNT "<img src=\"".$REPimages."r2.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep2/$case5)."></td>";
|
|
|
1513 }
|
|
|
1514 else {
|
|
|
1515 print HTMLCOUNT "<td class=\"ted\" style=\"border-left:3px solid black\">";
|
|
|
1516 print HTMLCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."<br>";
|
|
|
1517 print HTMLCOUNT "<img src=\"".$REPimages."r1.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep1/$case5).">";
|
|
|
1518 print HTMLCOUNT "<img src=\"".$REPimages."r2.png\" height=10 width=".sprintf("%.0f", $moyenneSNPindep2/$case5)."></td>";
|
|
|
1519 }
|
|
|
1520 print TABCOUNT sprintf("%.0f", $moyenneSNPindep1/$case5)."\t".sprintf("%.0f", $moyenneSNPindep2/$case5)."\t";
|
|
|
1521 }
|
|
|
1522 else {
|
|
|
1523 print HTMLCOUNT "<td style=\"border-left:3px solid black\"></td>";
|
|
|
1524 print TABCOUNT "\t";
|
|
|
1525 }
|
|
|
1526 print HTMLCOUNT "</tr>";
|
|
|
1527 print TABCOUNT "\n";
|
|
|
1528
|
|
|
1529 $totalSize = $totalSize + $taille_totale ;
|
|
|
1530 $totalSNP = $totalSNP + $taille ;
|
|
|
1531 $total11 = $total11 + $case1 ;
|
|
|
1532 $total22 = $total22 + $case2 ;
|
|
|
1533 $total3ou4 = $total3ou4 + $case3ou4 ;
|
|
|
1534 $total3 = $total3 + $case3 ;
|
|
|
1535 $total4 = $total4 + $case4 ;
|
|
|
1536 $total5 = $total5 + $case5 ;
|
|
|
1537 $total512 = $total512 + $total1 ;
|
|
|
1538 $total534 = $total534 + $total2 ;
|
|
|
1539 $totalOther = $totalOther + $caseOther ;
|
|
|
1540 $totalGenome2 = $totalGenome2 + $nbGenome2 ;
|
|
|
1541 }
|
|
|
1542 ########## MODIF DERNIERE MINUTE ################"
|
|
|
1543 print HTMLCOUNT "<tr class=\"td3\">\n<td>";
|
|
|
1544
|
|
|
1545 print HTMLCOUNT $nbTotGenesAna."<td style=\"border-left:3px solid black\">";
|
|
|
1546 print HTMLCOUNT $totalSize."</td><td style=\"border-left:3px solid black\">";
|
|
|
1547 print HTMLCOUNT $totalSNP."</td><td style=\"border-left:3px solid black\">";
|
|
|
1548 print HTMLCOUNT $total11."</td><td>";
|
|
|
1549 print HTMLCOUNT $total22."</td><td>";
|
|
|
1550 print HTMLCOUNT $total3ou4."</td><td>";
|
|
|
1551 print HTMLCOUNT $total3."</td><td>";
|
|
|
1552 print HTMLCOUNT $total4."</td><td>";
|
|
|
1553 print HTMLCOUNT $total5."</td><td>";
|
|
|
1554 print HTMLCOUNT $totalOther."</td><td style=\"border-left:3px solid black\">";
|
|
|
1555 print HTMLCOUNT $totalGenome2."</td><td style=\"border-left:3px solid black\">";
|
|
|
1556 print HTMLCOUNT $total512."</td><td style=\"border:3px solid black\">";
|
|
|
1557 print HTMLCOUNT $total534."</td><td style=\"border:3px solid black\">";
|
|
|
1558
|
|
|
1559 print HTMLCOUNT $nbTotGenesVal."</td>";
|
|
|
1560
|
|
|
1561 print HTMLCOUNT "</tr>";
|
|
|
1562
|
|
|
1563
|
|
|
1564 print TABCOUNT "$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";
|
|
|
1565 print TABCOUNT "\n";
|
|
|
1566
|
|
|
1567 ####################################################
|
|
|
1568 print HTMLSNP "</table>\n";
|
|
|
1569 print HTMLSNP "</html>\n";
|
|
|
1570 close HTMLSNP ;
|
|
|
1571
|
|
|
1572 print HTMLCOUNT "</table>\n";
|
|
|
1573 print HTMLCOUNT "</html>\n";
|
|
|
1574 close HTMLCOUNT ;
|
|
|
1575
|
|
|
1576 close TABSNP;
|
|
|
1577 close TABCOUNT ;
|
|
|
1578
|
|
|
1579 tie @array, 'Tie::File', $SNP_count or die ;
|
|
|
1580
|
|
|
1581 $array[113] = "<tr><td class=\"ted3\">".$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>";
|
|
|
1582 $array[114] = "<td class=\"ted3\" style=\"border-left:3px solid black\">";
|
|
|
1583 $array[115] = $total11."</td><td class=\"ted3\">".$total22."</td><td class=\"ted3\">".$total3ou4."</td><td class=\"ted3\">";
|
|
|
1584 $array[116] = $total3."</td><td class=\"ted3\">".$total4."</td><td class=\"ted3\">".$total5."</td><td class=\"ted3\">";
|
|
|
1585 $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>";
|
|
|
1586 $array[118] = "<td class=\"ted3\" style=\"border-left:3px solid black\">".$total534."</td><td class=\"ted3\">".$nbTotGenesVal."</td></tr>";
|
|
|
1587 }
|
|
|
1588
|
|
|
1589
|
|
|
1590
|
|
|
1591
|
|
|
1592 sub ext_output { # Extern reference
|
|
|
1593
|
|
|
1594 print TABCOUNT "Gene;Interval Size Analysed (pb);nb SNP;1;2;3 or 4;5;other;SNP Diploids;SNP Polyploid;Ratio (%) $genome2Name:$genome1Name\n";
|
|
|
1595
|
|
|
1596 foreach my $s(sort(keys(%snp))){
|
|
|
1597
|
|
|
1598 #######################################
|
|
|
1599 if ($ligneInter == 0) {
|
|
|
1600 print HTMLSNP "<tr class=\"bord1\">\n";
|
|
|
1601 print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n";
|
|
|
1602 }
|
|
|
1603 else {
|
|
|
1604 print HTMLSNP "<tr class=\"bord2\">\n";
|
|
|
1605 print HTMLCOUNT "<tr class=\"td2\">\n";
|
|
|
1606 }
|
|
|
1607 #######################################
|
|
|
1608
|
|
|
1609
|
|
|
1610 my $ref = $snp{$s};
|
|
|
1611 my %hash = %$ref;
|
|
|
1612 $taille = keys(%hash);
|
|
|
1613 # taille de la ligne gene
|
|
|
1614 print HTMLSNP "<td rowspan=\"$taille\"><b>$s</b></td>";
|
|
|
1615
|
|
|
1616 $ligneOK = 0 ;
|
|
|
1617
|
|
|
1618 $nbPolyploid = 0;
|
|
|
1619 $nbGenomes = 0 ;
|
|
|
1620 $nbCommuns = 0;
|
|
|
1621 $nbPoly_only = 0 ;
|
|
|
1622 $nbSub_only = 0 ;
|
|
|
1623
|
|
|
1624 $case5 = 0 ;
|
|
|
1625 $case1 = 0 ;
|
|
|
1626 $case2 = 0 ;
|
|
|
1627 $case3ou4 = 0;
|
|
|
1628 $caseOther = 0;
|
|
|
1629 $caseGenome2 = 0 ;
|
|
|
1630
|
|
|
1631 #Moyenne Ponderee
|
|
|
1632 $moyenneSNPindep1 = 0 ;
|
|
|
1633 $moyenneSNPindep2 = 0 ;
|
|
|
1634
|
|
|
1635 @tabTrie = sort ({ $a <=> $b }keys %hash);
|
|
|
1636
|
|
|
1637 #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) {
|
|
|
1638 foreach my $c(@tabTrie) {
|
|
|
1639 $nb1 = 0 ;
|
|
|
1640 $nb2 = 0 ;
|
|
|
1641 $nb3 = 0 ;
|
|
|
1642 if ($ligneOK == 1) {
|
|
|
1643 if ($ligneInter == 0) {
|
|
|
1644 print HTMLSNP "<tr class=\"td1\">\n";
|
|
|
1645 }
|
|
|
1646 else {
|
|
|
1647 print HTMLSNP "<tr class=\"td2\">\n";
|
|
|
1648 }
|
|
|
1649 }
|
|
|
1650 ### Recuperation des informations ###
|
|
|
1651 ($code_snp,$ratio,$GT_poly,$GT_G1,$GT_G2,$DP_P) = split(/\t/,$snp{$s}{$c});
|
|
|
1652 @recupAlleles = split(/\[/,$code_snp);
|
|
|
1653 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
1654 ($alRef,$alAlt) = split(/\//,$recupAlleles[0]);
|
|
|
1655 $noSNPpoly = "ok" ;
|
|
|
1656
|
|
|
1657 #print STDOUT "\n $c $GT_poly $GT_G1 $GT_G2";
|
|
|
1658 print HTMLSNP "<td>$c</td>";
|
|
|
1659 print TABSNP "$c;";
|
|
|
1660 #####################################################################
|
|
|
1661 # SNP POLYPLOID - [0/1] [0|1] [1|0]
|
|
|
1662 #####################################################################
|
|
|
1663 if (($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^1.0$/) ) { # Polyploid [0.1] [1.0]
|
|
|
1664 $ratio = sprintf("%.0f", $ratio);
|
|
|
1665 $ratio2 = 100-$ratio ;
|
|
|
1666 $moyenneSNPindep1 = $moyenneSNPindep1 + $ratio ;
|
|
|
1667 $moyenneSNPindep2 = $moyenneSNPindep2 + $ratio2 ;
|
|
|
1668 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1669 print TABSNP "$code_snp;";
|
|
|
1670 if (($GT_G1 =~ /^1.1$/)){ # Genome1 [1/1] [1|1]
|
|
|
1671 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1672 print TABSNP "$alAlt;";
|
|
|
1673 if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1]
|
|
|
1674 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1675 print HTMLSNP "<td></td>";
|
|
|
1676 print HTMLSNP "<td></td>";
|
|
|
1677 print HTMLSNP "<td></td>";
|
|
|
1678 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>";
|
|
|
1679 print TABSNP "$alAlt;";
|
|
|
1680 print TABSNP ";";
|
|
|
1681 print TABSNP ";";
|
|
|
1682 print TABSNP ";";
|
|
|
1683 print TABSNP "3 or 4;";
|
|
|
1684 }
|
|
|
1685 else {
|
|
|
1686 if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0]
|
|
|
1687 print HTMLSNP "<td>$alRef</td>";
|
|
|
1688 print HTMLSNP "<td>OK</td>";
|
|
|
1689 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1690 print HTMLSNP "<td></td>";
|
|
|
1691 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
|
|
|
1692 print TABSNP "$alRef";
|
|
|
1693 print TABSNP "OK";
|
|
|
1694 print TABSNP "[$ratio/$ratio2;]";
|
|
|
1695 print TABSNP "$DP_P;";
|
|
|
1696 print TABSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
|
|
|
1697 }
|
|
|
1698 else { # Genome2 = SNP [0.1]
|
|
|
1699 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1700 print HTMLSNP "<td>OK</td>";
|
|
|
1701 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1702 print HTMLSNP "<td></td>";
|
|
|
1703 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
|
|
|
1704 print TABSNP "$code_snp;";
|
|
|
1705 print TABSNP "OK;";
|
|
|
1706 print TABSNP "[$ratio/$ratio2];";
|
|
|
1707 print TABSNP "$DP_P;";
|
|
|
1708 print TABSNP "5';";
|
|
|
1709 }
|
|
|
1710 }
|
|
|
1711 }
|
|
|
1712 else{
|
|
|
1713 if ($GT_G1 =~ /^0.0$/){ # # Genome1 [0/0] [0|0]
|
|
|
1714 print HTMLSNP "<td>$alRef</td>";
|
|
|
1715 print TABSNP "$alRef;";
|
|
|
1716 if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1]
|
|
|
1717 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1718 print HTMLSNP "<td>OK</td>";
|
|
|
1719 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1720 print HTMLSNP "<td></td>";
|
|
|
1721 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
|
|
|
1722 print TABSNP "$alAlt;";
|
|
|
1723 print TABSNP "OK;";
|
|
|
1724 print TABSNP "[$ratio/$ratio2];";
|
|
|
1725 print TABSNP ";";
|
|
|
1726 print TABSNP "5;";
|
|
|
1727 }
|
|
|
1728 else {
|
|
|
1729 if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0]
|
|
|
1730 print HTMLSNP "<td>$alRef</td>";
|
|
|
1731 print HTMLSNP "<td></td>";
|
|
|
1732 print HTMLSNP "<td></td>";
|
|
|
1733 print HTMLSNP "<td></td>";
|
|
|
1734 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>";
|
|
|
1735 print TABSNP "$alRef;";
|
|
|
1736 print TABSNP ";";
|
|
|
1737 print TABSNP ";";
|
|
|
1738 print TABSNP ";";
|
|
|
1739 print TABSNP "3 or 4;";
|
|
|
1740 }
|
|
|
1741 else { # Genome2 = SNP [0.1]
|
|
|
1742 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1743 print HTMLSNP "<td>OK</td>";
|
|
|
1744 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1745 print HTMLSNP "<td></td>";
|
|
|
1746 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
|
|
|
1747 print TABSNP "$code_snp;";
|
|
|
1748 print TABSNP "OK;";
|
|
|
1749 print TABSNP "[$ratio/$ratio2];";
|
|
|
1750 print TABSNP ";";
|
|
|
1751 print TABSNP "5';";
|
|
|
1752 }
|
|
|
1753 }
|
|
|
1754 }
|
|
|
1755 else { # SNP Genome1 [0/1] [0|1] [1|0]
|
|
|
1756 print HTMLSNP "<td>$code_snp</td>"; #REF
|
|
|
1757 print HTMLSNP "$code_snp;"; #REF
|
|
|
1758 if($GT_G2 =~ /^1.1$/){ # Genome2 = Alt [1.1]
|
|
|
1759 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1760 print HTMLSNP "<td>OK</td>";
|
|
|
1761 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1762 print HTMLSNP "<td></td>";
|
|
|
1763 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
|
|
|
1764 print TABSNP "$alAlt;";
|
|
|
1765 print TABSNP "OK;";
|
|
|
1766 print TABSNP "[$ratio/$ratio2];";
|
|
|
1767 print TABSNP ";";
|
|
|
1768 print TABSNP "5'";
|
|
|
1769 }
|
|
|
1770 else {
|
|
|
1771 if($GT_G2 =~ /^0.0$/){ # Genome2 = Ref [0.0]
|
|
|
1772 print HTMLSNP "<td>$alRef</td>";
|
|
|
1773 print HTMLSNP "<td>OK</td>";
|
|
|
1774 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1775 print HTMLSNP "<td></td>";
|
|
|
1776 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5prime.png\" height=30></td>";
|
|
|
1777 print TABSNP "$alRef;";
|
|
|
1778 print TABSNP "OK;";
|
|
|
1779 print TABSNP "[$ratio/$ratio2];";
|
|
|
1780 print TABSNP ";";
|
|
|
1781 print TABSNP "5';";
|
|
|
1782 }
|
|
|
1783 else { # Genome2 = SNP [0.1]
|
|
|
1784 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1785 print HTMLSNP "<td></td>";
|
|
|
1786 print HTMLSNP "<td></td>";
|
|
|
1787 print HTMLSNP "<td></td>";
|
|
|
1788 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>";
|
|
|
1789 print TABSNP "$code_snp;";
|
|
|
1790 print TABSNP ";";
|
|
|
1791 print TABSNP ";";
|
|
|
1792 print TABSNP ";";
|
|
|
1793 print TABSNP "5''";
|
|
|
1794 }
|
|
|
1795 }
|
|
|
1796 }
|
|
|
1797 print TABSNP "\n";
|
|
|
1798 $ligneOK = 1 ;
|
|
|
1799 print HTMLSNP "</tr>\n";
|
|
|
1800 }
|
|
|
1801 }
|
|
|
1802 #####################################################################
|
|
|
1803 # POLYPLOID NE REFERENCE - [1/1]
|
|
|
1804 #####################################################################
|
|
|
1805 #print STDOUT "GTPOLY:$GT_poly@";
|
|
|
1806 if (($GT_poly =~ /^1.1$/) ) {
|
|
|
1807 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1808 print TABSNP "$alAlt;";
|
|
|
1809 ####################################
|
|
|
1810 if (($GT_G1 !~ /^0.0$/) && ($GT_G1 !~ /^1.1$/)){ # Genome 1 [0/1] [0|1] [1|0]
|
|
|
1811 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1812 print TABSNP "$code_snp";
|
|
|
1813 if ($GT_G2 =~ /^1.1$/) {
|
|
|
1814 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1815 print HTMLSNP "<td></td>";
|
|
|
1816 print HTMLSNP "<td></td>";
|
|
|
1817 print HTMLSNP "<td></td>";
|
|
|
1818 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
|
|
|
1819 print TABSNP "$alAlt;;;;5' or 1;";
|
|
|
1820 }
|
|
|
1821 else {
|
|
|
1822 if ($GT_G2 =~ /^0.0$/) {
|
|
|
1823 print HTMLSNP "<td>$alRef</td>";
|
|
|
1824 print HTMLSNP "<td></td>";
|
|
|
1825 print HTMLSNP "<td></td>";
|
|
|
1826 print HTMLSNP "<td></td>";
|
|
|
1827 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
|
|
|
1828 print TABSNP "$altRef;;;;5' or 1;";
|
|
|
1829 }
|
|
|
1830 else { # Genome2 = SNP [0.1]
|
|
|
1831 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1832 print HTMLSNP "<td></td>";
|
|
|
1833 print HTMLSNP "<td></td>";
|
|
|
1834 print HTMLSNP "<td></td>";
|
|
|
1835 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>";
|
|
|
1836 print TABSNP "$code_snp;;;;5'';";
|
|
|
1837 }
|
|
|
1838 }
|
|
|
1839 }
|
|
|
1840 else {
|
|
|
1841 if ($GT_G1 =~ /^0.0$/){ # Genome1 [0/0] [0|0]
|
|
|
1842 ###################
|
|
|
1843 print HTMLSNP "<td>$alRef</td>";
|
|
|
1844 print TABSNP "$alRef";
|
|
|
1845 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
|
|
|
1846 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1847 print HTMLSNP "<td></td>";
|
|
|
1848 print HTMLSNP "<td></td>";
|
|
|
1849 print HTMLSNP "<td></td>";
|
|
|
1850 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=30></td>";
|
|
|
1851 print TABSNP "$alAlt;;;;1;";
|
|
|
1852 }
|
|
|
1853 else {
|
|
|
1854 if ($GT_G2 =~ /^0.0$/) {
|
|
|
1855 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1856 print HTMLSNP "<td></td>";
|
|
|
1857 print HTMLSNP "<td></td>";
|
|
|
1858 print HTMLSNP "<td></td>";
|
|
|
1859 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."3ou4.png\" height=30></td>";
|
|
|
1860 print TABSNP "$alAlt;;;;3 or 4;";
|
|
|
1861 }
|
|
|
1862 else { # Genome2 = SNP [0.1]
|
|
|
1863 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1864 print HTMLSNP "<td></td>";
|
|
|
1865 print HTMLSNP "<td></td>";
|
|
|
1866 print HTMLSNP "<td></td>";
|
|
|
1867 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
|
|
|
1868 print TABSNP "$code_snp;;;;5' or 2";
|
|
|
1869 }
|
|
|
1870 }
|
|
|
1871 }
|
|
|
1872 else { # [1/1] [1|1] Genome 1
|
|
|
1873 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1874 print TABSNP "$alAlt";
|
|
|
1875 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
|
|
|
1876 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1877 print HTMLSNP "<td>OK</td>";
|
|
|
1878 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1879 print HTMLSNP "<td>$DP_P</td>";
|
|
|
1880 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5v.png\" height=30></td>";
|
|
|
1881 print TABSNP "$alAlt;OK;[$ratio/$ratio2];$DP_P;5;";
|
|
|
1882 }
|
|
|
1883 else {
|
|
|
1884 if ($GT_G2 =~ /^0.0$/) {
|
|
|
1885 print HTMLSNP "<td>$alRef</td>";
|
|
|
1886 print HTMLSNP "<td></td>";
|
|
|
1887 print HTMLSNP "<td></td>";
|
|
|
1888 print HTMLSNP "<td></td>";
|
|
|
1889 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=30></td>";
|
|
|
1890 print TABSNP "$alRef;;;;2;";
|
|
|
1891 }
|
|
|
1892 else { # Genome2 = SNP [0.1]
|
|
|
1893 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1894 print HTMLSNP "<td></td>";
|
|
|
1895 print HTMLSNP "<td></td>";
|
|
|
1896 print HTMLSNP "<td></td>";
|
|
|
1897 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
|
|
|
1898 print TABSNP "$code_snp;;;;5' or 2" ;
|
|
|
1899 }
|
|
|
1900 }
|
|
|
1901 }
|
|
|
1902 }
|
|
|
1903 $nbPolyploid ++ ;
|
|
|
1904 print TABSNP "\n";
|
|
|
1905 $ligneOK = 1 ;
|
|
|
1906 print HTMLSNP "</tr>\n";
|
|
|
1907
|
|
|
1908 }
|
|
|
1909 #####################################################################
|
|
|
1910 # POLYPLOID == REFERENCE - [0|0]
|
|
|
1911 #####################################################################
|
|
|
1912 if (($GT_poly =~ /^0.0$/) ) {
|
|
|
1913 print HTMLSNP "<td>$alRef</td>";
|
|
|
1914 print TABSNP "$alRef;";
|
|
|
1915 if (($GT_G1 !~ /^0.1$/) && ($GT_G1 !~ /^1.0$/)){ # Genome1 intra [0/1] [0|1] [1|0]
|
|
|
1916 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1917 print TABSNP "$code_snp";
|
|
|
1918 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
|
|
|
1919 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1920 print HTMLSNP "<td></td>";
|
|
|
1921 print HTMLSNP "<td></td>";
|
|
|
1922 print HTMLSNP "<td></td>";
|
|
|
1923 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
|
|
|
1924 print TABSNP "$alAlt;;;;5' or 1";
|
|
|
1925 }
|
|
|
1926 else {
|
|
|
1927 if ($GT_G2 =~ /^0.0$/) { # Genome2 = Ref [0.0]
|
|
|
1928 print HTMLSNP "<td>$alRef</td>";
|
|
|
1929 print HTMLSNP "<td></td>";
|
|
|
1930 print HTMLSNP "<td></td>";
|
|
|
1931 print HTMLSNP "<td></td>";
|
|
|
1932 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou1.png\" height=30></td>";
|
|
|
1933 print TABSNP "$alRef;;;;5' or 1";
|
|
|
1934 }
|
|
|
1935 else { # Genome2 = SNP [0.1]
|
|
|
1936 if ( ($GT_G2 =~ /^0.1$/) || ($GT_G2 =~ /^1.0$/)){ # Genome2 = SNP [0.1]
|
|
|
1937 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1938 print HTMLSNP "<td></td>";
|
|
|
1939 print HTMLSNP "<td></td>";
|
|
|
1940 print HTMLSNP "<td></td>";
|
|
|
1941 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5second.png\" height=30></td>";
|
|
|
1942 print TABSNP "$code_snp;;;;5''";
|
|
|
1943 }
|
|
|
1944 }
|
|
|
1945 }
|
|
|
1946 }
|
|
|
1947
|
|
|
1948 else {
|
|
|
1949 if ($GT_G1 =~ /^0.0$/){ # Pas de SNP Genome1 [0/0] [0|0]
|
|
|
1950 print HTMLSNP "<td>$alRef</td>";
|
|
|
1951 print TABSNP "$alRef";
|
|
|
1952 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
|
|
|
1953 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1954 print HTMLSNP "<td></td>";
|
|
|
1955 print HTMLSNP "<td></td>";
|
|
|
1956 print HTMLSNP "<td></td>";
|
|
|
1957 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."2.png\" height=30></td>";
|
|
|
1958 print TABSNP "$alAlt;;;;2;";
|
|
|
1959 }
|
|
|
1960 else {
|
|
|
1961 if ( ($GT_G2 =~ /^0.1$/) || ($GT_G2 =~ /^1.0$/)){
|
|
|
1962 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1963 print HTMLSNP "<td>OK</td>";
|
|
|
1964 print HTMLSNP "<td>[$ratio/$ratio2]</td>";
|
|
|
1965 print HTMLSNP "<td>$DP_P</td>";
|
|
|
1966 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
|
|
|
1967 print TABSNP "$code_snp;OK;[$ratio/$ratio2];$DP_P;5' or 2";
|
|
|
1968 }
|
|
|
1969 }
|
|
|
1970 }
|
|
|
1971
|
|
|
1972 else { # [1/1] [1|1] SNP entre genome1 et genome2
|
|
|
1973 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1974 print TABSNP "$alAlt";
|
|
|
1975 if ($GT_G2 =~ /^1.1$/) { # Genome2 = Alt [1.1]
|
|
|
1976 print HTMLSNP "<td>$alAlt</td>";
|
|
|
1977 print HTMLSNP "<td></td>";
|
|
|
1978 print HTMLSNP "<td></td>";
|
|
|
1979 print HTMLSNP "<td></td>";
|
|
|
1980 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."other.png\" height=30></td>";
|
|
|
1981 print TABSNP "$alAlt;;;;other;";
|
|
|
1982 }
|
|
|
1983 else {
|
|
|
1984 if ($GT_G2 =~ /^0.0$/) {
|
|
|
1985 print HTMLSNP "<td>$alRef</td>";
|
|
|
1986 print HTMLSNP "<td></td>";
|
|
|
1987 print HTMLSNP "<td></td>";
|
|
|
1988 print HTMLSNP "<td></td>";
|
|
|
1989 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."1.png\" height=30></td>";
|
|
|
1990 print TABSNP "$alRef;;;;1;";
|
|
|
1991 }
|
|
|
1992 else { # Genome2 = SNP [0.1]
|
|
|
1993 print HTMLSNP "<td>$code_snp</td>";
|
|
|
1994 print HTMLSNP "<td></td>";
|
|
|
1995 print HTMLSNP "<td></td>";
|
|
|
1996 print HTMLSNP "<td></td>";
|
|
|
1997 print HTMLSNP "<td class=\"final\"><img src=\"".$REPimages."5primeou2.png\" height=30></td>";
|
|
|
1998 print TABSNP "$code_snp;;;;5' or 2;";
|
|
|
1999 }
|
|
|
2000 }
|
|
|
2001 }
|
|
|
2002
|
|
|
2003 }
|
|
|
2004 }
|
|
|
2005 $nbSub_only ++;
|
|
|
2006 print TABSNP "\n";
|
|
|
2007 $ligneOK = 1 ;
|
|
|
2008 print HTMLSNP "</tr>\n";
|
|
|
2009 }
|
|
|
2010
|
|
|
2011 if ($ligneInter == 0) {
|
|
|
2012 print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">$s</td>";
|
|
|
2013 }
|
|
|
2014 else {
|
|
|
2015 print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">$s</td>";
|
|
|
2016 }
|
|
|
2017
|
|
|
2018 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;";
|
|
|
2019
|
|
|
2020 #######################################
|
|
|
2021 if ($ligneInter == 0) {
|
|
|
2022 $ligneInter = 1 ;
|
|
|
2023 }
|
|
|
2024 else {
|
|
|
2025 $ligneInter = 0 ;
|
|
|
2026 }
|
|
|
2027 #######################################
|
|
|
2028
|
|
|
2029 # Calcul des intervalles
|
|
|
2030 $taille_totale = 0 ;
|
|
|
2031 my $ref = $intervalle2{$s};
|
|
|
2032 my %hash = %$ref;
|
|
|
2033
|
|
|
2034 foreach my $interval(keys(%hash)){
|
|
|
2035 my @pos = split(/-/,$interval);
|
|
|
2036 $taille_inter = $pos[1]-$pos[0]-1 ;
|
|
|
2037 $taille_totale = $taille_totale + $taille_inter;
|
|
|
2038 }
|
|
|
2039
|
|
|
2040 $total1 = $case5 + $case1 + $case2 ;
|
|
|
2041 $total2 = $case5 + $case3ou4 ;
|
|
|
2042
|
|
|
2043 print HTMLCOUNT "<td>$taille_totale</td><td style=\"border-left:3px solid black\">$taille</td></td>";
|
|
|
2044 print HTMLCOUNT "<td style=\"border-left:3px solid black\">$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\">$total2</td>";
|
|
|
2045 if ($case5 != 0) {
|
|
|
2046 print HTMLCOUNT "<td style=\"border-left:3px solid black\">".sprintf("%.0f", $moyenneSNPindep1/$case5).":".sprintf("%.0f", $moyenneSNPindep2/$case5)."</td>";
|
|
|
2047 }
|
|
|
2048 else {
|
|
|
2049 print HTMLCOUNT "<td style=\"border-left:3px solid black\"></td>";
|
|
|
2050 }
|
|
|
2051 print HTMLCOUNT "</tr>";
|
|
|
2052
|
|
|
2053 $totalSize = $totalSize + $taille_totale ;
|
|
|
2054 $totalSNP = $totalSNP + $taille ;
|
|
|
2055 $total11 = $total11 + $case1 ;
|
|
|
2056 $total22 = $total22 + $case2 ;
|
|
|
2057 $total3ou4 = $total3ou4 + $case3ou4 ;
|
|
|
2058 $total5 = $total5 + $case5 ;
|
|
|
2059 $total512 = $total512 + $total1 ;
|
|
|
2060 $total534 = $total534 + $total2 ;
|
|
|
2061 $totalOther = $totalOther + $caseOther ;
|
|
|
2062 $totalGenome2 = $totalGenome2 + $caseGenome2 ;
|
|
|
2063 }
|
|
|
2064 ########## MODIF DERNIERE MINUTE ################"
|
|
|
2065 print HTMLCOUNT "<tr class=\"td3\">\n";
|
|
|
2066 print HTMLCOUNT "<td></td><td style=\"border-left:3px solid black\">$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>";
|
|
|
2067 print HTMLCOUNT "</tr>";
|
|
|
2068 ####################################################
|
|
|
2069 print HTMLSNP "</table>\n";
|
|
|
2070 print HTMLSNP "</html>\n";
|
|
|
2071 print HTMLCOUNT "</table>\n";
|
|
|
2072 print HTMLCOUNT "</html>\n";
|
|
|
2073
|
|
|
2074 close TABSNP;
|
|
|
2075 close HTMLSNP ;
|
|
|
2076 close HTMLCOUNT ;
|
|
|
2077 }
|
|
|
2078
|
|
|
2079 sub poly_poly_output {
|
|
|
2080 foreach my $s(sort(keys(%snp_final))){
|
|
|
2081 #######################################
|
|
|
2082 if ($ligneInter == 0) {
|
|
|
2083 print HTMLSNP "<tr class=\"bord1\">\n";
|
|
|
2084 print HTMLCOUNT "<tr class=\"td1\ border-width =\"3px\">\n";
|
|
|
2085 }
|
|
|
2086 else {
|
|
|
2087 print HTMLSNP "<tr class=\"bord2\">\n";
|
|
|
2088 print HTMLCOUNT "<tr class=\"td2\">\n";
|
|
|
2089 }
|
|
|
2090 #######################################
|
|
|
2091
|
|
|
2092 my $ref = $snp_final{$s};
|
|
|
2093 my %hash = %$ref;
|
|
|
2094 $taille = keys(%hash);
|
|
|
2095
|
|
|
2096 # taille de la ligne gene
|
|
|
2097 print HTMLSNP "<td rowspan=\"".$taille."\"><b>".$s."</b></td>";
|
|
|
2098
|
|
|
2099 $ligneOK = 0 ;
|
|
|
2100
|
|
|
2101 $nbPolyploid1 = 0 ; # SNP heterozygosity for P1
|
|
|
2102 $nbPolyploid2 = 0 ; # SNP heterozygosity for P2
|
|
|
2103 $nbCommuns = 0 ; # SNP heterozygosity [P1] = [P2]
|
|
|
2104 $nbCommunHomo = 0 ; # SNP homozygosity [P1] = [P2]
|
|
|
2105 $nbDifferent = 0 ; # [P1] ne [P2]
|
|
|
2106 $alleleCommun = 0 ; # Example : P1 = [A/G] ; P2 = [A]
|
|
|
2107 $alleleDifferent = 0 ; # Example : P1 = [A/G] ; P2 = [C] or [T]
|
|
|
2108 $alleleCommunH = 0 ; # Example : P1 = [A/G] ; P2 = [A/C]
|
|
|
2109 $nbHomoDiff = 0 ;
|
|
|
2110
|
|
|
2111 @tabTrie = sort ({ $a <=> $b }keys %hash);
|
|
|
2112
|
|
|
2113 $taille = 0;
|
|
|
2114
|
|
|
2115
|
|
|
2116
|
|
|
2117 #foreach my $c(sort ({$hash{$a} <=> $hash{$b}} keys %hash)) {
|
|
|
2118 foreach my $c(@tabTrie) {
|
|
|
2119
|
|
|
2120 if ($ligneOK == 1) {
|
|
|
2121 if ($ligneInter == 0) {
|
|
|
2122 print HTMLSNP "<tr class=\"td1\">\n";
|
|
|
2123 }
|
|
|
2124 else {
|
|
|
2125 print HTMLSNP "<tr class=\"td2\">\n";
|
|
|
2126 }
|
|
|
2127 }
|
|
|
2128
|
|
|
2129 #print STDOUT "\n\n\n".$snp_final{$s}{$c} ;
|
|
|
2130 ($code_snp,$AD,$GT_poly,$DP_P,$code_snp2,$AD_2,$GT_poly2,$DP_P2) = split(/\t/,$snp_final{$s}{$c});
|
|
|
2131 ($DP_P, $FDP) = split(/-/, $DP_P);
|
|
|
2132 ($DP_P2, $FDP2) = split(/-/, $DP_P2);
|
|
|
2133
|
|
|
2134 #print STDOUT "\nALLELES :".$AD." - ".$AD_2;
|
|
|
2135
|
|
|
2136 ($sub1_1,$sub1_2) = split(",",$AD);
|
|
|
2137 ($sub2_1,$sub2_2) = split(",",$AD_2);
|
|
|
2138
|
|
|
2139 # $sub1_1 = sprintf("%.0f", $sub1_1);
|
|
|
2140 # $sub1_2 = sprintf("%.0f", $sub1_2);
|
|
|
2141 # $sub2_1 = sprintf("%.0f", $sub2_1);
|
|
|
2142 # $sub2_2 = sprintf("%.0f", $sub2_2);
|
|
|
2143 if ($DP_P > 0) {
|
|
|
2144 $SG1 = ($sub1_1/$DP_P*100) ;
|
|
|
2145 $SG2 = ($sub1_2/$DP_P*100) ;
|
|
|
2146 }
|
|
|
2147 if ($DP_P2 > 0) {
|
|
|
2148 $SG3 = ($sub2_1/$DP_P2*100) ;
|
|
|
2149 $SG4 = ($sub2_2/$DP_P2*100) ;
|
|
|
2150 }
|
|
|
2151
|
|
|
2152
|
|
|
2153 if ($GT_poly ne "") { # Polyploide 1 = [0.0] ou [0.1] ou [1.1]
|
|
|
2154 @recupAlleles = split(/\[/,$code_snp);
|
|
|
2155 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
2156 ($alRef,$alAltP) = split(/\//,$recupAlleles[0]);
|
|
|
2157 # Attribution des alleles au polyploide 1 si pas de SNP
|
|
|
2158 if ($GT_poly =~ /^0.0$/) { $code_snp = $alRef ; }
|
|
|
2159 if ($GT_poly =~ /^1.1$/) { $code_snp = $alAltP ; }
|
|
|
2160 # Attribution des alleles au polyploide 2 si pas de SNP
|
|
|
2161 if (($GT_poly2 eq "") || ($GT_poly2 =~ /^0.0$/)) { $code_snp2 = $alRef ; }
|
|
|
2162 if ($GT_poly2 =~ /^1.1$/) {
|
|
|
2163 @recupAlleles = split(/\[/,$code_snp2);
|
|
|
2164 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
2165 ($alRef,$alAlt2) = split(/\//,$recupAlleles[0]);
|
|
|
2166 $code_snp2 = $alAlt2 ;
|
|
|
2167 }
|
|
|
2168 }
|
|
|
2169 elsif ($GT_poly2 ne "") { # pas de SNP polyploide 1 dans le fichier 1 (fichiers non mergés) -> equivalent de [0.0]
|
|
|
2170 @recupAlleles = split(/\[/,$code_snp2);
|
|
|
2171 @recupAlleles = split(/\]/,$recupAlleles[1]);
|
|
|
2172 ($alRef,$alAlt2) = split(/\//,$recupAlleles[0]);
|
|
|
2173 # Attribution des Alleles au polyploide 2
|
|
|
2174 if ($GT_poly2 =~ /^1.1$/) { $code_snp2 = $alAlt2 ; }
|
|
|
2175 if ($GT_poly2 =~ /^0.0$/) { $code_snp2 = $alRef ; }
|
|
|
2176 }
|
|
|
2177 #print STDOUT "\n($code_snp:$GT_poly) - ($code_snp2:$GT_poly2)" ;
|
|
|
2178 $noSNPpoly = "ok" ;
|
|
|
2179 #____________________________________________________________________________________________________________________________________________
|
|
|
2180 # [1] P1 = 0/1 ; P2 = 0/1 (2 alleles)
|
|
|
2181 #print STDOUT "\n".($code_snp2 eq $code_snp);
|
|
|
2182 if ((($GT_poly =~ /^0.1$/)||($GT_poly =~ /^1.0$/)) && (($GT_poly2 =~ /^0.1$/)||($GT_poly2 =~ /^1.0$/))) {
|
|
|
2183
|
|
|
2184 if (($SG1 > $value_filter_p1) && ($SG2 > $value_filter_p1) && ($SG3 > $value_filter_p2) && ($SG4 > $value_filter_p2) && $code_snp2 eq $code_snp) {
|
|
|
2185
|
|
|
2186
|
|
|
2187 if ($ligneInter == 0) {
|
|
|
2188
|
|
|
2189 print HTMLSNP "<td class=\"tedG2\">".$c."</td>";
|
|
|
2190 print HTMLSNP "<td class=\"tedG2\">".$alRef."</td>";
|
|
|
2191 print HTMLSNP "<td class=\"ted2\">".$code_snp."</td>";
|
|
|
2192 print HTMLSNP "<td class=\"ted2\">".$code_snp2."</td>";
|
|
|
2193
|
|
|
2194 print TABSNP $s . "\t";
|
|
|
2195 print TABSNP $c . "\t";
|
|
|
2196 print TABSNP $alRef . "\t";
|
|
|
2197 print TABSNP $code_snp . "\t";
|
|
|
2198 print TABSNP $code_snp2 . "\t";
|
|
|
2199 print TABSNP $FDP."/".$DP_P;
|
|
|
2200
|
|
|
2201 print HTMLSNP "<td class=\"ted2\">".$FDP."/".$DP_P;
|
|
|
2202 if (($DP_P) != 0) {
|
|
|
2203 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2204 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2205 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2206 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2207 }
|
|
|
2208 else {
|
|
|
2209 print HTMLSNP "</td>";
|
|
|
2210 print TABSNP "\t";
|
|
|
2211 }
|
|
|
2212
|
|
|
2213 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2214 print HTMLSNP "<td class=\"ted2\">".$FDP2."/".$DP_P2;
|
|
|
2215 if (($DP_P2) != 0) {
|
|
|
2216 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2217 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2218 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2219 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2220 }
|
|
|
2221 else {
|
|
|
2222 print HTMLSNP "</td>";
|
|
|
2223 print TABSNP "\t";
|
|
|
2224 }
|
|
|
2225 print TABSNP "\n";
|
|
|
2226 print HTMLSNP "</tr>\n";
|
|
|
2227 }
|
|
|
2228 else {
|
|
|
2229 #
|
|
|
2230 print HTMLSNP "<td class=\"tedG\">".$c."</td>";
|
|
|
2231 print HTMLSNP "<td class=\"tedG\">".$alRef."</td>";
|
|
|
2232 print HTMLSNP "<td class=\"ted\">".$code_snp."</td>";
|
|
|
2233 print HTMLSNP "<td class=\"ted\">".$code_snp2."</td>";
|
|
|
2234 print HTMLSNP "<td class=\"ted\">".$FDP." / ".$DP_P;
|
|
|
2235 print TABSNP $s . "\t";
|
|
|
2236 print TABSNP $c . "\t";
|
|
|
2237 print TABSNP $alRef . "\t";
|
|
|
2238 print TABSNP $code_snp . "\t";
|
|
|
2239 print TABSNP $code_snp2 . "\t";
|
|
|
2240 print TABSNP $FDP."/".$DP_P;
|
|
|
2241 if (($DP_P) != 0) {
|
|
|
2242 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2243 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2244 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2245 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2246 }
|
|
|
2247 else {
|
|
|
2248 print HTMLSNP "</td>";
|
|
|
2249 print TABSNP "\t";
|
|
|
2250 }
|
|
|
2251 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2252 print HTMLSNP "<td class=\"ted\">".$FDP2." / ".$DP_P2;
|
|
|
2253 if (($DP_P2) != 0) {
|
|
|
2254 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2255 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2256 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2257 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2258 }
|
|
|
2259 else {
|
|
|
2260 print HTMLSNP "</td>";
|
|
|
2261 print TABSNP "\t";
|
|
|
2262 }
|
|
|
2263 print TABSNP "\n";
|
|
|
2264 print HTMLSNP "</tr>\n";
|
|
|
2265 }
|
|
|
2266 $nbPolyploid1 ++ ; # SNP heterozygosity for P1
|
|
|
2267 $nbPolyploid2 ++ ; # SNP heterozygosity for P2
|
|
|
2268 $nbCommuns ++ ; # SNP heterozygosity [P1] = [P2]
|
|
|
2269 $taille++;
|
|
|
2270
|
|
|
2271 }
|
|
|
2272 else {
|
|
|
2273 if (($SG1 > $value_filter_p1) && ($SG2 > $value_filter_p1) && ($SG3 > $value_filter_p2) && ($SG4 > $value_filter_p2)) {
|
|
|
2274 if ($alAlt2 ne $alAlt) { # P1 [A/G] P2 [A/C] (3 alleles)
|
|
|
2275
|
|
|
2276
|
|
|
2277
|
|
|
2278 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2279 print HTMLSNP "<td style=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2280 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2281 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2282 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2283 print TABSNP $s . "\t";
|
|
|
2284 print TABSNP $c . "\t";
|
|
|
2285 print TABSNP $alRef . "\t";
|
|
|
2286 print TABSNP $code_snp . "\t";
|
|
|
2287 print TABSNP $code_snp2 . "\t";
|
|
|
2288 print TABSNP $FDP."/".$DP_P;
|
|
|
2289 if (($DP_P) != 0) {
|
|
|
2290 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2291 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2292 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2293 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2294 }
|
|
|
2295 else {
|
|
|
2296 print HTMLSNP "</td>";
|
|
|
2297 print TABSNP "\t";
|
|
|
2298 }
|
|
|
2299 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2300 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2301 if (($DP_P2) != 0) {
|
|
|
2302 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2303 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2304 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2305 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2306 }
|
|
|
2307 else {
|
|
|
2308 print HTMLSNP "</td>";
|
|
|
2309 print TABSNP "\t";
|
|
|
2310 }
|
|
|
2311 print TABSNP "\n";
|
|
|
2312 print HTMLSNP "</tr>\n";
|
|
|
2313 $nbDifferent ++ ;
|
|
|
2314 $alleleCommunH ++ ;
|
|
|
2315 $taille++;
|
|
|
2316 }
|
|
|
2317 }
|
|
|
2318 }
|
|
|
2319 }
|
|
|
2320
|
|
|
2321 else { # ALL
|
|
|
2322 # COMMON PART
|
|
|
2323 #print STDOUT "\nBOUM : ".$SG1." + ".$SG2." + ".$SG3." + ".$SG4 ;
|
|
|
2324 #if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1) && ($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) {
|
|
|
2325
|
|
|
2326 # print HTMLSNP "<td></td><td></td>";
|
|
|
2327
|
|
|
2328 # [5] P1 = 1/1 ; P2 = 1/1 (1 allele) P1 [A] P2 [A]
|
|
|
2329 if (($GT_poly =~ /^1.1$/) && ($GT_poly2 =~ /^1.1$/)) {
|
|
|
2330
|
|
|
2331
|
|
|
2332 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2333 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2334 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2335 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2336 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2337 print TABSNP $s . "\t";
|
|
|
2338 print TABSNP $c . "\t";
|
|
|
2339 print TABSNP $alRef . "\t";
|
|
|
2340 print TABSNP $code_snp . "\t";
|
|
|
2341 print TABSNP $code_snp2 . "\t";
|
|
|
2342 print TABSNP $FDP."/".$DP_P;
|
|
|
2343 if (($DP_P) != 0) {
|
|
|
2344 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2345 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2346 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2347 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2348 }
|
|
|
2349 else {
|
|
|
2350 print HTMLSNP "</td>";
|
|
|
2351 print TABSNP "\t";
|
|
|
2352 }
|
|
|
2353 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2354 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2355 if (($DP_P2) != 0) {
|
|
|
2356 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2357 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2358 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2359 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2360 }
|
|
|
2361 else {
|
|
|
2362 print HTMLSNP "</td>";
|
|
|
2363 print TABSNP "\t";
|
|
|
2364 }
|
|
|
2365 print TABSNP "\n";
|
|
|
2366 print HTMLSNP "</tr>\n";
|
|
|
2367 #*********************************************************************************************************************
|
|
|
2368 if ($code_snp2 eq $code_snp) {
|
|
|
2369 $nbCommunHomo ++ ;
|
|
|
2370 $taille++;
|
|
|
2371 }
|
|
|
2372 else { # (2 alleles) P1 [A] P2 [C]
|
|
|
2373 $nbDifferent ++ ;
|
|
|
2374 $nbHomoDiff ++ ;
|
|
|
2375 $taille++;
|
|
|
2376 }
|
|
|
2377 }
|
|
|
2378 # [2] [4] P1 = 0/1 ; P2 = 1/1
|
|
|
2379 if (((($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^0.1$/)) && ($GT_poly2 =~ /^1.1$/))) {
|
|
|
2380 if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1)) {
|
|
|
2381
|
|
|
2382
|
|
|
2383
|
|
|
2384 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2385 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2386 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2387 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2388 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2389 print TABSNP $s . "\t";
|
|
|
2390 print TABSNP $c . "\t";
|
|
|
2391 print TABSNP $alRef . "\t";
|
|
|
2392 print TABSNP $code_snp . "\t";
|
|
|
2393 print TABSNP $code_snp2 . "\t";
|
|
|
2394 print TABSNP $FDP."/".$DP_P;
|
|
|
2395 if (($DP_P) != 0) {
|
|
|
2396 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2397 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2398 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2399 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2400 }
|
|
|
2401 else {
|
|
|
2402 print HTMLSNP "</td>";
|
|
|
2403 print TABSNP "\t";
|
|
|
2404 }
|
|
|
2405 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2406 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2407 if (($DP_P2) != 0) {
|
|
|
2408 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2409 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2410 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2411 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2412 }
|
|
|
2413 else {
|
|
|
2414 print HTMLSNP "</td>";
|
|
|
2415 print TABSNP "\t";
|
|
|
2416 }
|
|
|
2417 print TABSNP "\n";
|
|
|
2418 print HTMLSNP "</tr>\n";
|
|
|
2419 if ($alAlt2 ne $alAlt) { # (2 alleles) P1 [A/G] P2 [G]
|
|
|
2420 $nbDifferent ++ ;
|
|
|
2421 $alleleCommun ++ ;
|
|
|
2422 $nbPolyploid1 ++ ;
|
|
|
2423 $taille++;
|
|
|
2424 }
|
|
|
2425 else { # (3 alleles) P1 [A/G] P2 [C]
|
|
|
2426 $nbDifferent ++ ;
|
|
|
2427 $alleleDifferent ++ ;
|
|
|
2428 $nbPolyploid1 ++ ;
|
|
|
2429 $taille++;
|
|
|
2430 }
|
|
|
2431 }
|
|
|
2432 }
|
|
|
2433 if ((($GT_poly2 =~ /^0.1$/) || ($GT_poly2 =~ /^0.1$/)) && ($GT_poly =~ /^1.1$/)) {
|
|
|
2434 if (($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) {
|
|
|
2435 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2436 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2437 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2438 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2439 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2440 print TABSNP $s . "\t";
|
|
|
2441 print TABSNP $c . "\t";
|
|
|
2442 print TABSNP $alRef . "\t";
|
|
|
2443 print TABSNP $code_snp . "\t";
|
|
|
2444 print TABSNP $code_snp2 . "\t";
|
|
|
2445 print TABSNP $FDP."/".$DP_P;
|
|
|
2446 if (($DP_P) != 0) {
|
|
|
2447 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2448 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2449 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2450 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2451 }
|
|
|
2452 else {
|
|
|
2453 print HTMLSNP "</td>";
|
|
|
2454 print TABSNP "\t";
|
|
|
2455 }
|
|
|
2456 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2457 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2458 if (($DP_P2) != 0) {
|
|
|
2459 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2460 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2461 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2462 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2463 }
|
|
|
2464 else {
|
|
|
2465 print HTMLSNP "</td>";
|
|
|
2466 print TABSNP "\t";
|
|
|
2467 }
|
|
|
2468 print TABSNP "\n";
|
|
|
2469 print HTMLSNP "</tr>\n";
|
|
|
2470 if ($alAlt2 ne $alAlt) { # (2 alleles) P1 [A/G] P2 [G]
|
|
|
2471 $nbDifferent ++ ;
|
|
|
2472 $alleleCommun ++ ;
|
|
|
2473 $nbPolyploid2 ++ ;
|
|
|
2474 $taille++;
|
|
|
2475 }
|
|
|
2476 else { # (3 alleles) P1 [A/G] P2 [C]
|
|
|
2477 $nbDifferent ++ ;
|
|
|
2478 $alleleDifferent ++ ;
|
|
|
2479 $nbPolyploid2 ++ ;
|
|
|
2480 $taille++;
|
|
|
2481 }
|
|
|
2482 }
|
|
|
2483 }
|
|
|
2484 # [3] [7] P1 = 0/1 ; P2 = 0/0 (2 alleles) P1 [A/G] P2 [A]
|
|
|
2485 if ((($GT_poly =~ /^0.1$/) || ($GT_poly =~ /^0.1$/)) && (($GT_poly2 =~ /^0.0$/) || ($GT_poly2 eq ""))) {
|
|
|
2486 if (($SG1> $value_filter_p1) && ($SG2> $value_filter_p1)) {
|
|
|
2487 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2488 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2489 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2490 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2491 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2492 print TABSNP $s . "\t";
|
|
|
2493 print TABSNP $c . "\t";
|
|
|
2494 print TABSNP $alRef . "\t";
|
|
|
2495 print TABSNP $code_snp . "\t";
|
|
|
2496 print TABSNP $code_snp2 . "\t";
|
|
|
2497 print TABSNP $FDP."/".$DP_P;
|
|
|
2498 if (($DP_P) != 0) {
|
|
|
2499 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2500 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2501 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2502 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2503 }
|
|
|
2504 else {
|
|
|
2505 print HTMLSNP "</td>";
|
|
|
2506 print TABSNP "\t";
|
|
|
2507 }
|
|
|
2508 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2509 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2510 if (($DP_P2) != 0) {
|
|
|
2511 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2512 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2513 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2514 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2515 }
|
|
|
2516 else {
|
|
|
2517 print HTMLSNP "</td>";
|
|
|
2518 print TABSNP "\t";
|
|
|
2519 }
|
|
|
2520 print TABSNP "\n";
|
|
|
2521 print HTMLSNP "</tr>\n";
|
|
|
2522
|
|
|
2523 $nbDifferent ++ ;
|
|
|
2524 $alleleCommun ++ ;
|
|
|
2525 $nbPolyploid1 ++ ;
|
|
|
2526 $taille++;
|
|
|
2527 }
|
|
|
2528 }
|
|
|
2529 if ((($GT_poly2 =~ /^0.1$/) || ($GT_poly2 =~ /^0.1$/)) && (($GT_poly =~ /^0.0$/) || ($GT_poly eq ""))) {
|
|
|
2530 if (($SG3> $value_filter_p2) && ($SG4> $value_filter_p2)) {
|
|
|
2531 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2532 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2533 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2534 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2535 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2536 print TABSNP $s . "\t";
|
|
|
2537 print TABSNP $c . "\t";
|
|
|
2538 print TABSNP $alRef . "\t";
|
|
|
2539 print TABSNP $code_snp . "\t";
|
|
|
2540 print TABSNP $code_snp2 . "\t";
|
|
|
2541 print TABSNP $FDP."/".$DP_P;
|
|
|
2542 if (($DP_P) != 0) {
|
|
|
2543 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2544 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2545 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2546 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2547 }
|
|
|
2548 else {
|
|
|
2549 print HTMLSNP "</td>";
|
|
|
2550 print TABSNP "\t";
|
|
|
2551 }
|
|
|
2552 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2553 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2554 if (($DP_P2) != 0) {
|
|
|
2555 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2556 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2557 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2558 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2559 }
|
|
|
2560 else {
|
|
|
2561 print HTMLSNP "</td>";
|
|
|
2562 print TABSNP "\t";
|
|
|
2563 }
|
|
|
2564 print TABSNP "\n";
|
|
|
2565 print HTMLSNP "</tr>\n";
|
|
|
2566 ############
|
|
|
2567 # HERE P2 #
|
|
|
2568 ############
|
|
|
2569 $nbDifferent ++ ;
|
|
|
2570 $alleleCommun ++ ;
|
|
|
2571 $nbPolyploid2 ++ ;
|
|
|
2572 $taille++;
|
|
|
2573 }
|
|
|
2574 }
|
|
|
2575 # [6] [8] P1 = 1/1 ; P2 = 0/0
|
|
|
2576 if (($GT_poly =~ /^1.1$/) && (($GT_poly2 =~ /^0.0$/) || ($GT_poly2 eq ""))) {
|
|
|
2577 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2578 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2579 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2580 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2581 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2582 print TABSNP $s . "\t";
|
|
|
2583 print TABSNP $c . "\t";
|
|
|
2584 print TABSNP $alRef . "\t";
|
|
|
2585 print TABSNP $code_snp . "\t";
|
|
|
2586 print TABSNP $code_snp2 . "\t";
|
|
|
2587 print TABSNP $FDP."/".$DP_P;
|
|
|
2588 if (($DP_P) != 0) {
|
|
|
2589 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2590 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2591 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2592 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2593 }
|
|
|
2594 else {
|
|
|
2595 print HTMLSNP "</td>";
|
|
|
2596 print TABSNP "\t";
|
|
|
2597 }
|
|
|
2598 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2599 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2600 if (($DP_P2) != 0) {
|
|
|
2601 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2602 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2603 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2604 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2605 }
|
|
|
2606 else {
|
|
|
2607 print HTMLSNP "</td>";
|
|
|
2608 print TABSNP "\t";
|
|
|
2609 }
|
|
|
2610 print TABSNP "\n";
|
|
|
2611 print HTMLSNP "</tr>\n";
|
|
|
2612 $nbDifferent ++ ;
|
|
|
2613 $alleleCommun ++ ;
|
|
|
2614 $nbPolyploid1 ++ ;
|
|
|
2615 $taille++;
|
|
|
2616 }
|
|
|
2617 if (($GT_poly2 =~ /^1.1$/) && (($GT_poly =~ /^0.0$/) || ($GT_poly eq ""))) {
|
|
|
2618 print HTMLSNP "<td style=\"border-left:3px solid black\">".$c."</td>";
|
|
|
2619 print HTMLSNP "<td class=\"border-left:3px solid black\">".$alRef."</td>";
|
|
|
2620 print HTMLSNP "<td>".$code_snp."</td>";
|
|
|
2621 print HTMLSNP "<td>".$code_snp2."</td>";
|
|
|
2622 print HTMLSNP "<td>".$FDP."/".$DP_P;
|
|
|
2623 print TABSNP $s . "\t";
|
|
|
2624 print TABSNP $c . "\t";
|
|
|
2625 print TABSNP $alRef . "\t";
|
|
|
2626 print TABSNP $code_snp . "\t";
|
|
|
2627 print TABSNP $code_snp2 . "\t";
|
|
|
2628 print TABSNP $FDP."/".$DP_P;
|
|
|
2629 if (($DP_P) != 0) {
|
|
|
2630 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP/$DP_P*100).">";
|
|
|
2631 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP/$DP_P*100).">";
|
|
|
2632 print HTMLSNP "<br>".$sub1_1." - ".$sub1_2."</td>";
|
|
|
2633 print TABSNP "," . $sub1_1." - ".$sub1_2."\t";
|
|
|
2634 }
|
|
|
2635 else {
|
|
|
2636 print HTMLSNP "</td>";
|
|
|
2637 print TABSNP "\t";
|
|
|
2638 }
|
|
|
2639 print TABSNP $FDP2."/".$DP_P2;
|
|
|
2640 print HTMLSNP "<td>".$FDP2."/".$DP_P2;
|
|
|
2641 if (($DP_P2) != 0) {
|
|
|
2642 print HTMLSNP "<br><img src=\"".$REPimages."r1.png\" height=5 width=".sprintf("%.0f", $FDP2/$DP_P2*100).">";
|
|
|
2643 print HTMLSNP "<img src=\"".$REPimages."r2.png\" height=5 width=".sprintf("%.0f", 100-$FDP2/$DP_P2*100).">";
|
|
|
2644 print HTMLSNP "<br>".$sub2_1." - ".$sub2_2."</td>";
|
|
|
2645 print TABSNP "," . $sub2_1." - ".$sub2_2."\t";
|
|
|
2646 }
|
|
|
2647 else {
|
|
|
2648 print HTMLSNP "</td>";
|
|
|
2649 print TABSNP "\t";
|
|
|
2650 }
|
|
|
2651 print TABSNP "\n";
|
|
|
2652 print HTMLSNP "</tr>\n";
|
|
|
2653 $nbDifferent ++ ;
|
|
|
2654 $alleleCommun ++ ;
|
|
|
2655 $nbPolyploid2 ++ ;
|
|
|
2656 $taille++;
|
|
|
2657 }
|
|
|
2658 #}
|
|
|
2659 }
|
|
|
2660
|
|
|
2661
|
|
|
2662 #print TABSNP $s."\t".$c."\t".$alRef."\t".$code_snp."\t".$code_snp2."\t".$FDP."\t".$DP_P."\t".$FDP2."\t".$DP_P2;
|
|
|
2663
|
|
|
2664 $ligneOK = 1 ;
|
|
|
2665 }
|
|
|
2666
|
|
|
2667
|
|
|
2668 if (($nbCommuns + $nbCommunHomo + $nbDifferent + $nbHomoDiff + $alleleCommun + $alleleDifferent + $alleleCommunH + $nbPolyploid1 + $nbPolyploid2) > 0 ) {
|
|
|
2669
|
|
|
2670 if ($ligneInter == 0) {
|
|
|
2671 print HTMLCOUNT "<td class=\"ted2\" style=\"border-right:3px solid black\">".$s."</td>";
|
|
|
2672 }
|
|
|
2673 else {
|
|
|
2674 print HTMLCOUNT "<td class=\"ted\" style=\"border-right:3px solid black\">".$s."</td>";
|
|
|
2675 }
|
|
|
2676 print TABCOUNT $s."\t";
|
|
|
2677
|
|
|
2678 #######################################
|
|
|
2679 if ($ligneInter == 0) { $ligneInter = 1 ; }
|
|
|
2680 else { $ligneInter = 0 ; }
|
|
|
2681 #######################################
|
|
|
2682
|
|
|
2683 # Calcul des intervalles #
|
|
|
2684 ##########################
|
|
|
2685 $taille_totale = 0 ;
|
|
|
2686 my $ref = $intervalle2{$s};
|
|
|
2687 my %hash = %$ref;
|
|
|
2688
|
|
|
2689 foreach my $interval(keys(%hash)){
|
|
|
2690 my @pos = split(/-/,$interval);
|
|
|
2691 $taille_inter = $pos[1]-$pos[0]+1 ;
|
|
|
2692 $taille_totale = $taille_totale + $taille_inter;
|
|
|
2693 }
|
|
|
2694 $total1 = $case5 + $case1 + $case2 + $casePolyplother;
|
|
|
2695 $total2 = $case5 + $case3ou4 + $caseDiplother;
|
|
|
2696
|
|
|
2697 # SYNTHESIS
|
|
|
2698
|
|
|
2699 print HTMLCOUNT "<td>".$taille_totale."</td><td style=\"border-left:3px solid black\">".$taille. "</td></td>";
|
|
|
2700 print HTMLCOUNT "<td style=\"border-left:3px solid black\">";
|
|
|
2701 print HTMLCOUNT $nbCommuns."</td><td>".$nbCommunHomo."</td><td style=\"border-left:3px solid black\">".$nbDifferent."</td><td style=\"border-left:3px solid black\">";
|
|
|
2702 print HTMLCOUNT $nbHomoDiff."</td><td>".$alleleCommun."</td><td>".$alleleDifferent."</td><td>".$alleleCommunH."</td>";
|
|
|
2703 print HTMLCOUNT "<td style=\"border-left:3px solid black\">".$nbPolyploid1."</td><td>".$nbPolyploid2."</td>";
|
|
|
2704 print TABCOUNT $taille_totale."\t".$taille."\t";
|
|
|
2705 print TABCOUNT $nbCommuns."\t".$nbCommunHomo."\t".$nbDifferent."\t".$nbHomoDiff."\t".$alleleCommun."\t".$alleleDifferent."\t".$alleleCommunH."\t".$nbPolyploid1."\t".$nbPolyploid2."\t";
|
|
|
2706
|
|
|
2707 $nbTotGenesAna ++ ;
|
|
|
2708
|
|
|
2709 print HTMLCOUNT "</tr>";
|
|
|
2710 print TABCOUNT "\n";
|
|
|
2711
|
|
|
2712 $totalSize = $totalSize + $taille_totale ;
|
|
|
2713 $totalSNP = $totalSNP + $taille ;
|
|
|
2714 $totalNbPolyploid1 = $totalNbPolyploid1 + $nbPolyploid1 ; # SNP heterozygosity for P1
|
|
|
2715 $totalNbPolyploid2 = $totalNbPolyploid2 + $nbPolyploid2 ; # SNP heterozygosity for P2
|
|
|
2716 $totalNbCommuns = $totalNbCommuns + $nbCommuns ; # SNP heterozygosity [P1] = [P2]
|
|
|
2717 $totalNbCommunsHomo = $totalNbCommunsHomo + $nbCommunHomo ; # SNP homozygosity [P1] = [P2]
|
|
|
2718 $totalNbDifferent = $totalNbDifferent + $nbDifferent ; # [P1] ne [P2]
|
|
|
2719 $totalNbAlleleCommun = $totalNbAlleleCommun + $alleleCommun ; # Example : P1 = [A/G] ; P2 = [A]
|
|
|
2720 $totalAlleleDifferent = $totalAlleleDifferent + $alleleDifferent ; # Example : P1 = [A/G] ; P2 = [C] or [T]
|
|
|
2721 $totalAlleleCommunH = $totalAlleleCommunH + $alleleCommunH ; # Example : P1 = [A/G] ; P2 = [A/C]
|
|
|
2722 $totalNbHomoDiff = $totalNbHomoDiff + $nbHomoDiff ; # Example : P1 = [A/G] ; P2 = [A/C]
|
|
|
2723 }
|
|
|
2724
|
|
|
2725
|
|
|
2726
|
|
|
2727
|
|
|
2728 }
|
|
|
2729 ########## MODIF DERNIERE MINUTE ################"
|
|
|
2730 print HTMLCOUNT "<tr class=\"td3\">\n<td>";
|
|
|
2731
|
|
|
2732 print HTMLCOUNT $nbTotGenesAna."<td style=\"border-left:3px solid black\">";
|
|
|
2733 print HTMLCOUNT $totalSize."</td><td style=\"border-left:3px solid black\">";
|
|
|
2734 print HTMLCOUNT $totalSNP."</td><td style=\"border-left:3px solid black\">";
|
|
|
2735 print HTMLCOUNT $totalNbCommuns."</td><td>";
|
|
|
2736 print HTMLCOUNT $totalNbCommunsHomo."</td><td>";
|
|
|
2737 print HTMLCOUNT $totalNbDifferent."</td><td style=\"border-left:3px solid black\">";
|
|
|
2738 print HTMLCOUNT $totalNbHomoDiff."</td><td style=\"border-left:3px solid black\">";
|
|
|
2739 print HTMLCOUNT $totalNbAlleleCommun."</td><td style=\"border:3px solid black\">";
|
|
|
2740 print HTMLCOUNT $totalAlleleDifferent."</td><td style=\"border:3px solid black\">";
|
|
|
2741 print HTMLCOUNT $totalAlleleCommunH."</td><td>";
|
|
|
2742 print HTMLCOUNT $totalNbPolyploid1."</td><td>";
|
|
|
2743 print HTMLCOUNT $totalNbPolyploid2."</td>";
|
|
|
2744 print HTMLCOUNT "</tr>";
|
|
|
2745
|
|
|
2746
|
|
|
2747 print TABCOUNT "$nbTotGenesAna\t$totalSize\t$totalSNP\t$totalNbCommuns\t$totalNbCommunsHomo\t$totalNbDifferent\t$totalNbHomoDiff\t$totalNbAlleleCommun\t$totalAlleleDifferent\t$totalAlleleCommunH\t$totalNbPolyploid1\t$totalNbPolyploid2\t";
|
|
|
2748 print TABCOUNT "\n";
|
|
|
2749
|
|
|
2750 ####################################################
|
|
|
2751 print HTMLSNP "</table>\n";
|
|
|
2752 print HTMLSNP "</html>\n";
|
|
|
2753 close HTMLSNP ;
|
|
|
2754
|
|
|
2755 print HTMLCOUNT "</table>\n";
|
|
|
2756 print HTMLCOUNT "</html>\n";
|
|
|
2757 close HTMLCOUNT ;
|
|
|
2758
|
|
|
2759 close TABSNP;
|
|
|
2760 close TABCOUNT ;
|
|
|
2761
|
|
|
2762 # tie @array, 'Tie::File', $SNP_count or die ;
|
|
|
2763 # $array[82] = "<table class=\"tab2\"><th class=\"th\" style=\"text-align:left;\">";
|
|
|
2764 # $array[83] = "<br>".$nbTotGenesAna." analysed genes";
|
|
|
2765 # $array[84] = "<br>".$nbTotGenesVal." with SNP validation";
|
|
|
2766 # $array[85] = "<br>Analysis performed on ".$totalSize." bp";
|
|
|
2767 # $array[86] = "<br>".$totalSNP." SNP";
|
|
|
2768 # $array[87] = "<br><img src=\"".$REPimages."5v.png\" WIDTH=20> : ".$total5." validated SNP";
|
|
|
2769 # $array[88] = "<br><br><img src=\"".$REPimages."1.png\" WIDTH=20> : ".$total11."";
|
|
|
2770 # $array[89] = "<br><img src=\"".$REPimages."2.png\" WIDTH=20> : ".$total22."";
|
|
|
2771 # $array[90] = "<br><img src=\"".$REPimages."3ou4.png\" WIDTH=20> : ".$total3ou4."";
|
|
|
2772 # $array[91] = "<br>Other SNP types : ".$totalOther."";
|
|
|
2773 # $array[92] = "<br>Heterozygosity for genome 1 : ".$totalGenome2."";
|
|
|
2774 # $array[93] = "<br>SNP between parental genomes (diploids) : ".$total512."";
|
|
|
2775 # $array[94] = "<br>SNP polyploid : ".$total534."";
|
|
|
2776 # $array[95] = "<th class=\"th\"><img src=\"".$REPimages."arbre.png\" WIDTH=400></th></table>";
|
|
|
2777 }
|
|
|
2778
|
|
|
2779 $time2 = time ;
|
|
|
2780 $tmps = $time2 - $time;
|
|
|
2781 print STDOUT "\n\nTemps execution : ".$tmps."\n";
|
