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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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1
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1 package CPT::Bio::NW_MSA;
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2 use Moose;
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3 use strict;
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4 use warnings;
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5 use autodie;
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6 use List::Util qw(max);
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7
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8 has 'sequences' => ( is => 'rw', isa => 'ArrayRef');
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9 # If true, relationships are assumed to be bidirectional
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10 has 'bidi' => (is => 'rw', isa => 'Bool');
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11 has 'relationships' => ( is => 'rw', isa => 'HashRef', default => sub { {} });
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12 #
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13 has 'verbose' => ( is => 'rw', isa => 'Num');
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14 #
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15 has 'gap_penalty' => ( is => 'rw', isa => 'Num');
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16 has 'match_score' => ( is => 'rw', isa => 'Num');
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17 has 'mismatch_score' => ( is => 'rw', isa => 'Num');
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18
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19 # local stuff
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20 #has 'current_list' => ( is => 'rw', isa => 'ArrayRef');
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21 has 'merger' => (is => 'rw', isa => 'HashRef');
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22 has 'number_of_aligned_lists' => ( is => 'rw', isa => 'Num', default => sub { 0 });
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23
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24 sub add_relationship {
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25 my ($self, $from, $to) = @_;
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26 ${$self->relationships()}{$from}{$to} = 1;
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27 if($self->bidi()){
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28 ${$self->relationships()}{$to}{$from} = 1;
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29 }
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30 }
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31
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32 sub Sij {
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33 my($self, $merger_row, $query) = @_;
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34 # Comparing a query against a merger row
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35 my @check_against = @{$merger_row};
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36 #print "Checking " . join(",",@check_against) .":$query\t";
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37 foreach(@check_against){
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38 if(${$self->relationships()}{$query}{$_}
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39 || ${$self->relationships()}{$_}{$query}){
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40 #print $self->match_score() . "\n";
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41 return $self->match_score();
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42 }
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43 }
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44 #print $self->mismatch_score() . "\n";
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45 return $self->mismatch_score();
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46 }
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47
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48 sub align_list {
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49 my ($self, $list_ref) = @_;
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50 # If we haven't aligned any lists, we do something special
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51 if($self->number_of_aligned_lists() == 0){
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52 # Pretend we've aligned ONE list already
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53 $self->number_of_aligned_lists(1);
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54 my @list = @{$list_ref};
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55 # Fake the merger
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56 my %merger;
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57 for(my $i = 0; $i < scalar @list; $i++){
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58 $merger{$i} = [$list[$i]];
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59 }
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60 $self->merger(\%merger);
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61 }else{
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62 $self->find_best_path($self->merger(), $list_ref);
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63 $self->number_of_aligned_lists($self->number_of_aligned_lists() + 1);
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64 }
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65 }
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66
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67 sub find_best_path {
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68 my ($self, $merger_ref, $list_ref) = @_;
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69 my %merger = %{$merger_ref};
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70 my @list = @{$list_ref};
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71
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72 my $max_i = scalar(keys(%merger));
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73 my $max_j = scalar(@list);
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74
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75 my %score_mat;
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76 my %point_mat;
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77
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78 # Initial zeros for matrices
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79 $point_mat{0}{0} = 'DONE';
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80 $score_mat{0}{0} = 0;
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81
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82 for(my $a = 1; $a <= $max_i; $a++){
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83 $point_mat{$a}{0} = 'U';
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84 $score_mat{$a}{0} = $self->gap_penalty();
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85 }
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86 for(my $b = 1; $b <= $max_j; $b++){
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87 $point_mat{0}{$b} = 'L';
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88 $score_mat{0}{$b} = $self->gap_penalty();
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89 }
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90
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91 # Score
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92 for(my $i = 1 ; $i <= $max_i; $i++){
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93 my $ci = $merger{$i-1};
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94 for(my $j = 1; $j <= $max_j; $j++){
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95 my $cj = $list[$j-1];
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96 # Scoring
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97 my $diag_score = $score_mat{$i-1}{$j-1} + $self->Sij($ci,$cj);
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98 my $up_score = $score_mat{$i-1}{$j} + $self->gap_penalty();
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99 my $left_score = $score_mat{$i}{$j-1} + $self->gap_penalty();
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100
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101 if($diag_score >= $up_score){
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102 if($diag_score >= $left_score){
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103 $score_mat{$i}{$j} = $diag_score;
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104 $point_mat{$i}{$j} = 'D';
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105 }else{
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106 $score_mat{$i}{$j} = $left_score;
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107 $point_mat{$i}{$j} = 'L';
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108 }
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109 }else{
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110 if($up_score >= $left_score){
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111 $score_mat{$i}{$j} = $up_score;
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112 $point_mat{$i}{$j} = 'U';
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113 }else{
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114 $score_mat{$i}{$j} = $left_score;
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115 $point_mat{$i}{$j} = 'L';
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116 }
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117 }
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118 }
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119 }
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120
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121 $self->print2DArray('score_mat', \%score_mat);
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122 $self->print2DArray('point_mat', \%point_mat);
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123
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124
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125 # Calculate merger
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126 my @new_row_set;
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127 my $i = $max_i + 0;
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128 my $j = $max_j + 0;
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129 while($i != 0 || $j != 0){
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130 my $dir = $point_mat{$i}{$j};
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131 my @new_row;
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132 if($dir eq 'D'){
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133 push(@new_row, @{$merger{$i-1}}, $list[$j-1]);
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134 $i--;
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135 $j--;
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136 }elsif($dir eq 'L'){
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137 push(@new_row, split(//, '-' x ($self->number_of_aligned_lists())));
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138 push(@new_row, $list[$j-1]);
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139 $j--;
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140 }elsif($dir eq 'U'){
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141 push(@new_row, @{$merger{$i-1}}, '-');
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142 $i--;
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143 }
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144 if($self->verbose()){
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145 print join("\t", $i, $j, $dir, @new_row),"\n";
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146 }
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147 push(@new_row_set,\@new_row);
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148 }
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149
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150 my %new_merger;
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151 for(my $i = 0; $i < scalar(@new_row_set); $i++){
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152 $new_merger{$i} = $new_row_set[scalar(@new_row_set) - $i - 1];
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153 }
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154 $self->merger(\%new_merger);
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155 }
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156
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157 sub merged_array{
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158 my ($self) = @_;
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159 my %m = %{$self->merger()};
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160 my @result;
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161 foreach(sort{$a<=>$b} keys(%m)){
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162 push(@result, $m{$_});
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163 }
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164 return @result;
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165 }
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166
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167
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168 sub print2DArray{
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169 my($self,$name, $ref) = @_;
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170 if($self->verbose && defined $ref){
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171 print '*' x 32,"\n";
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172 print $name,"\n";
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173 if(ref $ref eq 'ARRAY'){
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174 foreach(@{$ref}){
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175 print join("\t",@{$_}),"\n";
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176 }
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177 }elsif(ref $ref eq 'HASH'){
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178 my %h = %{$ref};
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179 foreach my $a(sort(keys(%h))){
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180 if(ref $h{$a} eq 'ARRAY'){
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181 print join("", map { sprintf "%-4s",$_ } @{$h{$a}});
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182 }else{
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183 foreach my $b(sort(keys($h{$a}))){
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184 if(defined($h{$a}{$b})){
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185 printf "%5s", $h{$a}{$b};
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186 }
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187 }
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188 }
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189 print "\n";
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190 }
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191 }else{
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192 die 'Unsupported';
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193 }
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194 print '*' x 32,"\n";
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195 }
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196 }
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197
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198
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199 no Moose;
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200 1;
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201
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202 __END__
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203
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204 =pod
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205
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206 =encoding UTF-8
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207
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208 =head1 NAME
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209
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210 CPT::Bio::NW_MSA
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211
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212 =head1 VERSION
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213
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214 version 1.99.4
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215
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216 =head1 AUTHOR
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217
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218 Eric Rasche <rasche.eric@yandex.ru>
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219
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220 =head1 COPYRIGHT AND LICENSE
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221
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222 This software is Copyright (c) 2014 by Eric Rasche.
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223
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224 This is free software, licensed under:
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225
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226 The GNU General Public License, Version 3, June 2007
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227
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228 =cut