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planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:48:47 +0000
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0:54c7a3ea81e2 1:8691c1c61a8e
1 package CPT::Bio::NW_MSA;
2 use Moose;
3 use strict;
4 use warnings;
5 use autodie;
6 use List::Util qw(max);
7
8 has 'sequences' => ( is => 'rw', isa => 'ArrayRef');
9 # If true, relationships are assumed to be bidirectional
10 has 'bidi' => (is => 'rw', isa => 'Bool');
11 has 'relationships' => ( is => 'rw', isa => 'HashRef', default => sub { {} });
12 #
13 has 'verbose' => ( is => 'rw', isa => 'Num');
14 #
15 has 'gap_penalty' => ( is => 'rw', isa => 'Num');
16 has 'match_score' => ( is => 'rw', isa => 'Num');
17 has 'mismatch_score' => ( is => 'rw', isa => 'Num');
18
19 # local stuff
20 #has 'current_list' => ( is => 'rw', isa => 'ArrayRef');
21 has 'merger' => (is => 'rw', isa => 'HashRef');
22 has 'number_of_aligned_lists' => ( is => 'rw', isa => 'Num', default => sub { 0 });
23
24 sub add_relationship {
25 my ($self, $from, $to) = @_;
26 ${$self->relationships()}{$from}{$to} = 1;
27 if($self->bidi()){
28 ${$self->relationships()}{$to}{$from} = 1;
29 }
30 }
31
32 sub Sij {
33 my($self, $merger_row, $query) = @_;
34 # Comparing a query against a merger row
35 my @check_against = @{$merger_row};
36 #print "Checking " . join(",",@check_against) .":$query\t";
37 foreach(@check_against){
38 if(${$self->relationships()}{$query}{$_}
39 || ${$self->relationships()}{$_}{$query}){
40 #print $self->match_score() . "\n";
41 return $self->match_score();
42 }
43 }
44 #print $self->mismatch_score() . "\n";
45 return $self->mismatch_score();
46 }
47
48 sub align_list {
49 my ($self, $list_ref) = @_;
50 # If we haven't aligned any lists, we do something special
51 if($self->number_of_aligned_lists() == 0){
52 # Pretend we've aligned ONE list already
53 $self->number_of_aligned_lists(1);
54 my @list = @{$list_ref};
55 # Fake the merger
56 my %merger;
57 for(my $i = 0; $i < scalar @list; $i++){
58 $merger{$i} = [$list[$i]];
59 }
60 $self->merger(\%merger);
61 }else{
62 $self->find_best_path($self->merger(), $list_ref);
63 $self->number_of_aligned_lists($self->number_of_aligned_lists() + 1);
64 }
65 }
66
67 sub find_best_path {
68 my ($self, $merger_ref, $list_ref) = @_;
69 my %merger = %{$merger_ref};
70 my @list = @{$list_ref};
71
72 my $max_i = scalar(keys(%merger));
73 my $max_j = scalar(@list);
74
75 my %score_mat;
76 my %point_mat;
77
78 # Initial zeros for matrices
79 $point_mat{0}{0} = 'DONE';
80 $score_mat{0}{0} = 0;
81
82 for(my $a = 1; $a <= $max_i; $a++){
83 $point_mat{$a}{0} = 'U';
84 $score_mat{$a}{0} = $self->gap_penalty();
85 }
86 for(my $b = 1; $b <= $max_j; $b++){
87 $point_mat{0}{$b} = 'L';
88 $score_mat{0}{$b} = $self->gap_penalty();
89 }
90
91 # Score
92 for(my $i = 1 ; $i <= $max_i; $i++){
93 my $ci = $merger{$i-1};
94 for(my $j = 1; $j <= $max_j; $j++){
95 my $cj = $list[$j-1];
96 # Scoring
97 my $diag_score = $score_mat{$i-1}{$j-1} + $self->Sij($ci,$cj);
98 my $up_score = $score_mat{$i-1}{$j} + $self->gap_penalty();
99 my $left_score = $score_mat{$i}{$j-1} + $self->gap_penalty();
100
101 if($diag_score >= $up_score){
102 if($diag_score >= $left_score){
103 $score_mat{$i}{$j} = $diag_score;
104 $point_mat{$i}{$j} = 'D';
105 }else{
106 $score_mat{$i}{$j} = $left_score;
107 $point_mat{$i}{$j} = 'L';
108 }
109 }else{
110 if($up_score >= $left_score){
111 $score_mat{$i}{$j} = $up_score;
112 $point_mat{$i}{$j} = 'U';
113 }else{
114 $score_mat{$i}{$j} = $left_score;
115 $point_mat{$i}{$j} = 'L';
116 }
117 }
118 }
119 }
120
121 $self->print2DArray('score_mat', \%score_mat);
122 $self->print2DArray('point_mat', \%point_mat);
123
124
125 # Calculate merger
126 my @new_row_set;
127 my $i = $max_i + 0;
128 my $j = $max_j + 0;
129 while($i != 0 || $j != 0){
130 my $dir = $point_mat{$i}{$j};
131 my @new_row;
132 if($dir eq 'D'){
133 push(@new_row, @{$merger{$i-1}}, $list[$j-1]);
134 $i--;
135 $j--;
136 }elsif($dir eq 'L'){
137 push(@new_row, split(//, '-' x ($self->number_of_aligned_lists())));
138 push(@new_row, $list[$j-1]);
139 $j--;
140 }elsif($dir eq 'U'){
141 push(@new_row, @{$merger{$i-1}}, '-');
142 $i--;
143 }
144 if($self->verbose()){
145 print join("\t", $i, $j, $dir, @new_row),"\n";
146 }
147 push(@new_row_set,\@new_row);
148 }
149
150 my %new_merger;
151 for(my $i = 0; $i < scalar(@new_row_set); $i++){
152 $new_merger{$i} = $new_row_set[scalar(@new_row_set) - $i - 1];
153 }
154 $self->merger(\%new_merger);
155 }
156
157 sub merged_array{
158 my ($self) = @_;
159 my %m = %{$self->merger()};
160 my @result;
161 foreach(sort{$a<=>$b} keys(%m)){
162 push(@result, $m{$_});
163 }
164 return @result;
165 }
166
167
168 sub print2DArray{
169 my($self,$name, $ref) = @_;
170 if($self->verbose && defined $ref){
171 print '*' x 32,"\n";
172 print $name,"\n";
173 if(ref $ref eq 'ARRAY'){
174 foreach(@{$ref}){
175 print join("\t",@{$_}),"\n";
176 }
177 }elsif(ref $ref eq 'HASH'){
178 my %h = %{$ref};
179 foreach my $a(sort(keys(%h))){
180 if(ref $h{$a} eq 'ARRAY'){
181 print join("", map { sprintf "%-4s",$_ } @{$h{$a}});
182 }else{
183 foreach my $b(sort(keys($h{$a}))){
184 if(defined($h{$a}{$b})){
185 printf "%5s", $h{$a}{$b};
186 }
187 }
188 }
189 print "\n";
190 }
191 }else{
192 die 'Unsupported';
193 }
194 print '*' x 32,"\n";
195 }
196 }
197
198
199 no Moose;
200 1;
201
202 __END__
203
204 =pod
205
206 =encoding UTF-8
207
208 =head1 NAME
209
210 CPT::Bio::NW_MSA
211
212 =head1 VERSION
213
214 version 1.99.4
215
216 =head1 AUTHOR
217
218 Eric Rasche <rasche.eric@yandex.ru>
219
220 =head1 COPYRIGHT AND LICENSE
221
222 This software is Copyright (c) 2014 by Eric Rasche.
223
224 This is free software, licensed under:
225
226 The GNU General Public License, Version 3, June 2007
227
228 =cut