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1 #!/usr/bin/perl -w
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2 use strict;
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3
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4 # Define variables
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5 my @temp=();
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6 my $result1;
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7 my $result2;
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8 my $result3;
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9 my $result4;
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10 my $result5;
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11 my $result6;
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12 my $resultfinal;
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13 my $count;
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14 my $coun;
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15 my $cou;
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16 my @digit=();
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17 my $digit;
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18 my $marks;
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19 my $log;
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20 my $coll;
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21 my @scorearray=();
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22 my $scorearray;
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23 my $percent;
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24 my $kount;
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25 my @result=();
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26 my $result;
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27 my %final=();
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28 my $final;
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29 my @c=();
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30 my @matrix1;
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31 my @matrix2;
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32 my $matrix1;
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33 my $matrix2;
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34 $coll=0;
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35 my $count2;
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36 my $var;
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37 my $entry1;
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38 my $entry2;
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39 my $reventry1;
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40 my $reventry2;
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41 my $revvar;
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42 my @revmatrix1;
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43 my $revkount;
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44 my $revcoun;
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45 my $revcount2;
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46 my @revtemp;
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47 my $revcoll;
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48 my @revdigit;
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49 my $revdigit;
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50 my $revmarks;
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51 my $revresult1;
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52 my $revresult2;
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53 my $revresult3;
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54 my $revresult4;
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55 my $revresult5;
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56 my $revresult6;
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57 my $revresultfinal;
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58 my @revscorearray;
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59 my $revscorearray;
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60
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61
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62
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63 #define variables from configuration file
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64 open (IN, "<$ARGV[0]");
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65 open (IN2, "<$ARGV[1]");
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66 open (OUT, ">$ARGV[2]");
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67
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68 #assign arrays to variables from configuration file
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69 my @array5=<IN>;
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70
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71 my @coordinates=<IN2>;
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72
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73
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74 #split the chromosome number and starting position from coordinates file into 2 separate strings
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75
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76 foreach my $coordinates(@coordinates) {
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77
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78 chomp($coordinates);
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79
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80 my @coordinates2=split(/\s+/, $coordinates);
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81
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82 my $coordinates2;
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83
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84 $entry1=$coordinates2[0];
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85 $entry2=$coordinates2[1];
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86
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87 }
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88
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89
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90 print OUT "CTCF Site", "\t", "Chromosome no.", "\t", "Start", "\t", "End", "\t", "Score", "\t", "Strand", "\n";
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91
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92 chomp (@array5);
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93
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94 my $digits=join("", @array5);
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95
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96 my @yeslap = $digits =~ /(?=(\w\w\w\w\w\w\w\w\w\w\w\w\w\w\w\w\w\w\w))/g;
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97
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98
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99 $var = "@yeslap\n";
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100
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101
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102 @matrix1=qw/87.25 291.25 76.25 459.25 167.25 145.25 414.25 187.25 281.25 49.25 449.25 134.25 56.25 800.25 21.25 36.25 8.25 903.25 0.25 2.25 744.25 13.25 65.25 91.25 40.25 528.25 334.25 11.25 107.25 433.25 48.25 324.25 851.25 11.25 32.25 18.25 5.25 0.25 903.25 3.25 333.25 3.25 566.25 9.25 54.25 12.25 504.25 341.25 12.25 0.25 890.25 8.25 56.25 8.25 775.25 71.25 104.25 733.25 5.25 67.25 372.25 13.25 507.25 17.25 82.25 482.25 307.25 37.25 117.25 322.25 73.25 396.25 402.25 181.25 266.25 59.25/;
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103
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104 $kount=0;
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105 $coun=0;
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106
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107 # Define the pattern for CTCF. Because of pseudocount, a wildcard is allowed at
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108 #each position.
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109 my $pattern = "[ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC][ATGC]";
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110
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111 # Compare the pattern with the 19 bp nucleotide segments.
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112
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113 while($var =~ m/$pattern/gi)
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114 {
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115 $coun++;
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116 $count2++;
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117 my $endpos = pos $var;
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118
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119 # Get the starting and ending positions of the matched pattern.
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120
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121 my $startpos=($endpos+1)-19;
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122 my $lastpos=$endpos;
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123
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124
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125 my $consensus = substr($var, ($startpos-1), 19);
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126
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127 push(@temp, $consensus, $startpos, $lastpos);
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128
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129 $coll=0;
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130 $kount++;
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131
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132
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133 # Split the matched pattern into 19 single bases.
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134
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135 @digit = split(//, $consensus);
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136
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137
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138 # For each base, if the base is A, calculate the weight score of A according to
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139 #its frequency in the CTCF Position Frequency Matrix.
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140 foreach $digit (@digit)
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141 {
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142
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143
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144 if($digit =~ m/A/)
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145 {
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146
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147
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148 my $ref = \@matrix1;
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149 $marks = @{$ref}[$coll];
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150
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151
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152 $result1 = sqrt(914);
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153
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154 $result2 = $result1*0.3;
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155
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156 $result3 = $result2+$marks;
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157 $result4 = sqrt(914);
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158 $result5 = $result4+914;
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159 $result6 = 0.3;
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160
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161 $resultfinal = log($result3/$result5/$result6)/log(2);
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162
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163
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164
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165
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166
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167 push(@scorearray, $resultfinal);
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168
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169
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170
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171 }
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172
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173 if($digit =~ m/C/)
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174
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175 {
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176
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177 my $ref = \@matrix1;
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178
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179 $marks = @{$ref}[$coll + 1];
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180
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181 $result1 = sqrt(914);
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182 $result2 = $result1*0.2;
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183 $result3 = $result2+$marks;
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184 $result4 = sqrt(914);
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185 $result5 = $result4+914;
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186 $result6 = 0.2;
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187
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188 $resultfinal = log($result3/$result5/$result6)/log(2);
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189
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190 push(@scorearray, $resultfinal);
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191
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192
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193 }
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194
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195
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196 if($digit =~ m/G/)
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197
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198 {
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199
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200 my $ref = \@matrix1;
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201
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202 $marks = @{$ref}[$coll+2];
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203
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204 $result1 = sqrt(914);
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205 $result2 = $result1*0.2;
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206 $result3 = $result2+$marks;
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207 $result4 = sqrt(914);
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208 $result5 = $result4+914;
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209 $result6 = 0.2;
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210
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211 $resultfinal = log($result3/$result5/$result6)/log(2);
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212
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213
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214 push(@scorearray, $resultfinal);
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215
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216 }
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217
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218 if($digit =~ m/T/)
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219
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220 {
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221
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222 my $ref = \@matrix1;
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223
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224 $marks = @{$ref}[$coll+3];
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225
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226 $result1 = sqrt(914);
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227 $result2 = $result1*0.3;
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228 $result3 = $result2+$marks;
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229 $result4 = sqrt(914);
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230 $result5 = $result4+914;
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231 $result6 = 0.3;
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232
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233 $resultfinal = log($result3/$result5/$result6)/log(2);
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234
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235
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236 push(@scorearray, $resultfinal);
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237
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238 }
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239
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240 $coll=$coll + 4;
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241
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242 }
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243
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244 @digit=();
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245 my $tem=0;
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246
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247
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248 foreach $scorearray(@scorearray)
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249 {
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250
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251 $tem = $tem + $scorearray;
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252
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253
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254 }
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255
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256 @scorearray = ();
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257
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258
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259 my $fpercent = $tem;
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260
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261
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262 if ($fpercent >= 18) {
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263
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264 print OUT $consensus, "\t", $entry1, "\t", $count2 + $entry2, "\t", $count2 + $entry2 + 18, "\t", "$fpercent", "\t", "+", "\n";
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265
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266
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267 }
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268
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269 }
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270
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271
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272 close ( OUT );
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273 close ( IN );
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274 close ( IN2 );
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