Mercurial > repos > dereeper > vcftools_filter_stats_diversity
annotate VCFToolsSlidingWindow/VCFToolsSlidingWindow.pl @ 3:151a9aec4607 draft
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author | dereeper |
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date | Sun, 04 Feb 2024 14:19:20 +0000 |
parents | 7130bd0d2a83 |
children | 3ae4c598ac08 |
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1 |
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2 #!/usr/bin/perl |
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3 |
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4 use strict; |
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5 use Getopt::Long; |
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6 use Bio::SeqIO; |
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7 |
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8 my $usage = qq~Usage:$0 <args> [<opts>] |
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9 |
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10 where <args> are: |
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11 |
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12 -i, --input <VCF input> |
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13 -o, --out <output basename> |
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14 -w, --window <window size> |
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15 |
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16 <opts> are: |
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17 -g, --group <group file> |
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18 ~; |
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19 $usage .= "\n"; |
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20 |
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21 my ($input,$out); |
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22 my $window = 200000; |
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23 my $groupfile; |
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24 GetOptions( |
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25 "input=s" => \$input, |
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26 "out=s" => \$out, |
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27 "window=s" => \$window, |
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28 "group=s" => \$groupfile |
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29 ); |
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30 |
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31 |
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32 |
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33 die $usage |
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34 if ( !$input); |
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35 |
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36 my %hash; |
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37 my $cmd_part = ""; |
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38 if ($groupfile && -e $groupfile) |
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39 { |
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40 open(my $G,$groupfile) or die "Cannot open $groupfile: $!"; |
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41 while(<$G>) |
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42 { |
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43 my $line = $_; |
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44 chomp($line); |
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45 $line=~s/\r//g; |
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46 $line=~s/\n//g; |
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47 my @infos = split(/;/,$line); |
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48 if ($infos[0] && $infos[1]) |
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49 { |
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50 $hash{$infos[1]} .= " --indv " . $infos[0]; |
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51 $cmd_part .= " --indv " . $infos[0]; |
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52 } |
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53 } |
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54 close($G); |
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55 } |
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56 |
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57 |
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58 if ($window =~/^(\d+)\s*$/){ |
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59 $window = $1; |
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60 } |
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61 else{ |
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62 die "Error: window size must be an integer\n"; |
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63 } |
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64 |
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65 |
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66 my $input_format = "--vcf $input.sorted"; |
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67 if ($input =~/\.vcf/){ |
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68 system("vcf-sort $input >$input.sorted"); |
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69 $input_format = "--vcf $input.sorted"; |
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70 } |
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71 elsif ($input =~/\.bcf/){ |
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72 $input_format = "--bcf $input"; |
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73 } |
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74 system("vcftools $input_format --out $out --window-pi $window --window-pi-step $window >>$out.vcftools.log 2>&1"); |
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75 system("vcftools $input_format --out $out --TajimaD $window >>$out.vcftools.log 2>&1"); |
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76 system("vcftools $input_format --out $out --TsTv $window >>$out.vcftools.log 2>&1"); |
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77 system("vcftools $input_format --out $out --SNPdensity $window >>$out.vcftools.log 2>&1"); |
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78 |
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79 |
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80 |
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81 ################################################## |
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82 # Tajima distribution |
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83 ################################################## |
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84 my %counts3; |
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85 my @values; |
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86 open(my $TAJIMA,"$out.Tajima.D"); |
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87 <$TAJIMA>; |
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88 my $max = 0; |
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89 while(<$TAJIMA>){ |
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90 my $line = $_; |
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91 $line =~s/\n//g; |
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92 $line =~s/\r//g; |
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93 my @inf = split(/\t/,$line); |
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94 my $val = $inf[3]; |
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95 my $arrondi = sprintf("%.1f",$val); |
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96 $counts3{$arrondi}++; |
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97 } |
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98 close($TAJIMA); |
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99 |
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100 |
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101 my %counts3_pop; |
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102 |
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103 if (keys(%hash) > 0) |
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104 { |
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105 my $files_pi = ""; |
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106 my $files_dtajima = ""; |
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107 my $cmd_fst = "--fst-window-size $window"; |
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108 my $cmd_fst_by_marker = ""; |
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109 foreach my $pop(sort(keys(%hash))) |
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110 { |
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111 my $cmd_part = $hash{$pop}; |
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112 |
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113 |
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114 open(my $POP,">$input.$pop.txt"); |
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115 my @ind_of_pop = split(" --indv ",$cmd_part); |
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116 print $POP join("\n",@ind_of_pop); |
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117 close($POP); |
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118 $cmd_fst .= " --weir-fst-pop $input.$pop.txt"; |
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119 $cmd_fst_by_marker .= " --weir-fst-pop $input.$pop.txt"; |
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120 |
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121 my $cmd_part = $hash{$pop}; |
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122 system("vcftools $input_format --remove-filtered-all --out $out.$pop --window-pi $window --window-pi-step $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); |
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123 my $sed_cmd = "sed -i \"s\/PI\/$pop\/g\" $out.$pop.windowed.pi"; |
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124 system($sed_cmd); |
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125 $files_pi .= "$out.$pop.windowed.pi "; |
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126 |
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127 system("vcftools $input_format --remove-filtered-all --out $out.$pop --SNPdensity $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); |
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128 |
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129 system("vcftools $input_format --remove-filtered-all --out $out.$pop --TajimaD $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); |
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130 my $sed_cmd = "sed -i \"s\/TajimaD\/$pop\/g\" $out.$pop.Tajima.D"; |
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131 system($sed_cmd); |
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132 $sed_cmd = "sed -i \"s/nan/0/g\" $out.Tajima.D"; |
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133 system($sed_cmd); |
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134 $files_dtajima .= "$out.$pop.Tajima.D "; |
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135 |
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136 |
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137 open(my $TAJIMAPOP,"$out.$pop.Tajima.D"); |
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138 <$TAJIMAPOP>; |
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139 my $max = 0; |
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140 while(<$TAJIMAPOP>){ |
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141 my $line = $_; |
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142 $line =~s/\n//g; |
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143 $line =~s/\r//g; |
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144 my @inf = split(/\t/,$line); |
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145 my $val = $inf[3]; |
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146 my $arrondi = sprintf("%.1f",$val); |
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147 $counts3_pop{$pop}{$arrondi}++; |
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148 } |
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149 close($TAJIMAPOP); |
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150 |
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151 system("vcftools $input_format --remove-filtered-all --out $out.$pop --TsTv $window $cmd_part --maf 0.001 >>$out.vcftools.log 2>&1"); |
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152 } |
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153 system("paste $files_pi >$out.combined.pi"); |
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154 my $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$5\"\t\"\$10'} $out.combined.pi >$out.combined.pi.txt"; |
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155 system($awk_cmd); |
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156 |
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157 system("paste $files_dtajima >>$out.combined.dtajima"); |
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158 $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$4\"\t\"\$8'} $out.combined.dtajima >$out.combined.dtajima.txt"; |
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159 system($awk_cmd); |
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160 |
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161 system("vcftools $input_format --remove-filtered-all --out $out.fst $cmd_fst --maf 0.001 >>$out.vcftools.log 2>&1"); |
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162 $awk_cmd = "awk {'print \$1\"\t\"\$2\"\t\"\$5'} $out.fst.windowed.weir.fst >$out.fst.txt"; |
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163 system($awk_cmd); |
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164 |
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165 system("vcftools $input_format --remove-filtered-all --out $out.fst $cmd_fst_by_marker --maf 0.001 >>$out.vcftools.log 2>&1"); |
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166 |
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167 my %genes; |
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168 open(my $V,$input); |
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169 my $go = 0; |
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170 while(<$V>){ |
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171 if ($go){ |
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172 my @infos = split(/\t/,$_); |
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173 my $chr = $infos[0]; |
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174 my $pos = $infos[1]; |
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175 my $annot = $infos[7]; |
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176 my $gene = "#"; |
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177 if ($annot =~/EFF=\w+\((.*)\)/){ |
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178 my @parts = split(/\|/,$1); |
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179 $gene = $parts[4]; |
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180 } |
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181 $genes{"$chr:$pos"} = $gene; |
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182 } |
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183 if (/^#CHROM/){$go = 1;} |
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184 } |
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185 |
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186 my $cumul = 0; |
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187 my $previous_pos; |
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188 my %chrs; |
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189 |
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190 # get only the first 2000 points |
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191 `sort -k 3 $out.fst.weir.fst | grep -v 'nan' | grep -v 'e-' | tail -10001 | sort -n -k 2 >$out.fst.weir.highest.fst`; |
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192 |
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193 my %hash; |
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194 open(my $F,"$out.fst.weir.highest.fst"); |
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195 <$F>; |
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196 open(my $O,">$out.fst.by_marker.txt"); |
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197 open(my $O2,">$out.fst.by_marker.genes.txt"); |
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198 print $O "Chromosome Marker Position Fst\n"; |
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199 print $O2 "Chromosome Marker Position Fst\n"; |
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200 while(<$F>){ |
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201 my $line = $_; |
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202 chomp($line); |
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203 my ($chr,$pos,$val) = split(/\t/,$line); |
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204 $hash{$chr}{$pos} = $val; |
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205 } |
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206 close($F); |
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207 foreach my $chr(sort keys(%hash)){ |
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208 my $ref_hash = $hash{$chr}; |
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209 my %hash2 = %$ref_hash; |
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210 foreach my $pos(sort {$a<=>$b} keys(%hash2)){ |
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211 my $val = $hash{$chr}{$pos}; |
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212 if (!$chrs{$chr}){ |
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213 $cumul = $previous_pos; |
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214 $chrs{$chr} = 1; |
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215 } |
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216 my $x = $pos+$cumul; |
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217 #print $O2 "$chr $chr:$pos $pos $val " . $genes{"$chr:$pos"} . "\n"; |
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218 print $O2 "$chr $chr:$pos $pos $val\n"; |
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219 print $O "$chr $chr:$pos $x $val\n"; |
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220 $previous_pos = $x; |
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221 } |
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222 |
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223 } |
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224 |
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225 close($O); |
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226 close($O2); |
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227 |
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228 #$awk_cmd = "awk {'if (\$3>0.6 && \$3<=1 && \$3!~\"nan\"){print \$1\"\t\"\$2\"\t\"\$2\"\t\"\$3}'} $out.fst.weir.fst >$out.fst.by_marker.txt"; |
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229 #system($awk_cmd); |
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230 } |
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231 open(my $M3,">$out.tajima_distrib"); |
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232 print $M3 "Values nb of values"; |
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233 if (keys(%hash) > 0){ |
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234 print $M3 " ".join("\t",keys(%hash)); |
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235 } |
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236 print $M3 "\n"; |
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237 for (my $i = -2.5; $i <= 2.5; $i=$i+0.1) |
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238 { |
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239 my $arrondi = sprintf("%.1f",$i); |
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240 my $nb = 0; |
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241 if ($counts3{$arrondi}) |
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242 { |
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243 $nb = $counts3{$arrondi}; |
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244 } |
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245 print $M3 "Tajima $arrondi $nb"; |
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246 if (keys(%hash) > 0){ |
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247 foreach my $pop(sort(keys(%hash))){ |
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248 my $nb_pop = 0; |
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249 if ($counts3_pop{$pop}{$arrondi}){ |
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250 $nb_pop = $counts3_pop{$pop}{$arrondi}; |
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251 } |
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252 print $M3 " $nb_pop"; |
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253 } |
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254 } |
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255 print $M3 "\n"; |
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256 } |
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257 close($M3); |
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258 |
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259 |
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260 |
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261 |
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262 |