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1 | package Text::Tradition::StemmaUtil; |
2 | |
3 | use strict; |
4 | use warnings; |
5 | use Exporter 'import'; |
6 | use vars qw/ @EXPORT_OK /; |
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7 | use Bio::Phylo::IO; |
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8 | use Encode qw( decode_utf8 ); |
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9 | use File::chdir; |
10 | use File::Temp; |
11 | use File::Which; |
12 | use Graph; |
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13 | use IPC::Run qw/ run binary /; |
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14 | use Text::Tradition::Error; |
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15 | use Text::Tradition::Stemma; |
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16 | @EXPORT_OK = qw/ character_input phylip_pars parse_newick newick_to_svg /; |
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17 | |
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18 | =head1 NAME |
19 | |
20 | Text::Tradition::StemmaUtil - standalone utilities for distance tree calculations |
21 | |
22 | =head1 DESCRIPTION |
23 | |
24 | This package contains a set of utilities for running phylogenetic analysis on |
25 | text collations. |
26 | |
27 | =head1 SUBROUTINES |
28 | |
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29 | =head2 character_input( $tradition, $opts ) |
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30 | |
31 | Returns a character matrix string suitable for Phylip programs, which |
32 | corresponds to the given alignment table. See Text::Tradition::Collation |
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33 | for a description of the alignment table format. Options include: |
34 | |
35 | =over |
36 | |
37 | =item * exclude_layer - Exclude layered witnesses from the character input, |
38 | using only the 'main' text of the witnesses in the tradition. |
39 | |
40 | =item * collapse - A reference to an array of relationship names that should |
41 | be treated as equivalent for the purposes of generating the character matrix. |
42 | |
43 | =back |
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44 | |
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45 | =cut |
46 | |
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47 | sub character_input { |
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48 | my ( $tradition, $opts ) = @_; |
49 | my $table = $tradition->collation->alignment_table; |
50 | if( $opts->{exclude_layer} ) { |
51 | # Filter out all alignment table rows that do not correspond |
52 | # to a named witness - these are the layered witnesses. |
53 | my $newtable = { alignment => [] }; |
54 | foreach my $row ( $table->{alignment} ) { |
55 | if( $tradition->has_witness( $row->{witness} ) ) { |
56 | push( @{$newtable->{alignment}}, $row ); |
57 | } |
58 | } |
59 | $table = $newtable; |
60 | } |
61 | my $character_matrix = _make_character_matrix( $table, $opts ); |
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62 | my $input = ''; |
63 | my $rows = scalar @{$character_matrix}; |
64 | my $columns = scalar @{$character_matrix->[0]} - 1; |
65 | $input .= "\t$rows\t$columns\n"; |
66 | foreach my $row ( @{$character_matrix} ) { |
67 | $input .= join( '', @$row ) . "\n"; |
68 | } |
69 | return $input; |
70 | } |
71 | |
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72 | sub _make_character_matrix { |
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73 | my( $table, $opts ) = @_; |
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74 | # Push the names of the witnesses to initialize the rows of the matrix. |
75 | my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] } |
76 | @{$table->{'alignment'}}; |
77 | foreach my $token_index ( 0 .. $table->{'length'} - 1) { |
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78 | my @pos_tokens = map { $_->{'tokens'}->[$token_index] } |
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79 | @{$table->{'alignment'}}; |
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80 | my @pos_readings = map { $_ ? $_->{'t'} : $_ } @pos_tokens; |
81 | my @chars = _convert_characters( \@pos_readings, $opts ); |
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82 | foreach my $idx ( 0 .. $#matrix ) { |
83 | push( @{$matrix[$idx]}, $chars[$idx] ); |
84 | } |
85 | } |
86 | return \@matrix; |
87 | } |
88 | |
89 | # Helper function to make the witness name something legal for pars |
90 | |
91 | sub _normalize_witname { |
92 | my( $witname ) = @_; |
93 | $witname =~ s/\s+/ /g; |
94 | $witname =~ s/[\[\]\(\)\:;,]//g; |
95 | $witname = substr( $witname, 0, 10 ); |
96 | return sprintf( "%-10s", $witname ); |
97 | } |
98 | |
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99 | sub _convert_characters { |
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100 | my( $row, $opts ) = @_; |
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101 | # This is a simple algorithm that treats every reading as different. |
102 | # Eventually we will want to be able to specify how relationships |
103 | # affect the character matrix. |
104 | my %unique = ( '__UNDEF__' => 'X', |
105 | '#LACUNA#' => '?', |
106 | ); |
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107 | my %equivalent; |
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108 | my %count; |
109 | my $ctr = 0; |
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110 | foreach my $rdg ( @$row ) { |
111 | next unless $rdg; |
112 | next if $rdg->is_lacuna; |
113 | next if exists $unique{$rdg->text}; |
114 | if( ref( $opts->{'collapse'} ) eq 'ARRAY' ) { |
115 | my @exclude_types = @{$opts->{'collapse'}}; |
116 | my @set = $rdg->related_readings( sub { my $rel = shift; |
117 | $rel->colocated && grep { $rel->type eq $_ } @exclude_types } ); |
118 | push( @set, $rdg ); |
119 | my $char = chr( 65 + $ctr++ ); |
120 | map { $unique{$_->text} = $char } @set; |
121 | $count{$rdg->text} += scalar @set; |
122 | } else { |
123 | $unique{$rdg->text} = chr( 65 + $ctr++ ); |
124 | $count{$rdg->text}++; |
125 | } |
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126 | } |
127 | # Try to keep variants under 8 by lacunizing any singletons. |
128 | if( scalar( keys %unique ) > 8 ) { |
129 | foreach my $word ( keys %count ) { |
130 | if( $count{$word} == 1 ) { |
131 | $unique{$word} = '?'; |
132 | } |
133 | } |
134 | } |
135 | my %u = reverse %unique; |
136 | if( scalar( keys %u ) > 8 ) { |
137 | warn "Have more than 8 variants on this location; phylip will break"; |
138 | } |
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139 | my @chars = map { $_ ? $unique{$_->text} : $unique{'__UNDEF__' } } @$row; |
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140 | return @chars; |
141 | } |
142 | |
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143 | =head2 phylip_pars( $character_matrix ) |
144 | |
145 | Runs Phylip Pars on the given character matrix. Returns results in Newick format. |
146 | |
147 | =cut |
148 | |
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149 | sub phylip_pars { |
150 | my( $charmatrix ) = @_; |
151 | # Set up a temporary directory for all the default Phylip files. |
152 | my $phylip_dir = File::Temp->newdir(); |
153 | # $phylip_dir->unlink_on_destroy(0); |
154 | # We need an infile, and we need a command input file. |
155 | open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile"; |
156 | print MATRIX $charmatrix; |
157 | close MATRIX; |
158 | |
159 | open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile"; |
160 | ## TODO any configuration parameters we want to set here |
161 | # U Search for best tree? Yes |
162 | # S Search option? More thorough search |
163 | # V Number of trees to save? 100 |
164 | # J Randomize input order of species? No. Use input order |
165 | # O Outgroup root? No, use as outgroup species 1 |
166 | # T Use Threshold parsimony? No, use ordinary parsimony |
167 | # W Sites weighted? No |
168 | # M Analyze multiple data sets? No |
169 | # I Input species interleaved? Yes |
170 | # 0 Terminal type (IBM PC, ANSI, none)? ANSI |
171 | # 1 Print out the data at start of run No |
172 | # 2 Print indications of progress of run Yes |
173 | # 3 Print out tree Yes |
174 | # 4 Print out steps in each site No |
175 | # 5 Print character at all nodes of tree No |
176 | # 6 Write out trees onto tree file? Yes |
177 | print CMD "Y\n"; |
178 | close CMD; |
179 | |
180 | # And then we run the program. |
181 | my $program = File::Which::which( 'pars' ); |
182 | unless( -x $program ) { |
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183 | throw( "Phylip pars not found in path" ); |
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184 | } |
185 | |
186 | { |
187 | # We need to run it in our temporary directory where we have created |
188 | # all the expected files. |
189 | local $CWD = $phylip_dir; |
190 | my @cmd = ( $program ); |
191 | run \@cmd, '<', 'cmdfile', '>', '/dev/null'; |
192 | } |
193 | # Now our output should be in 'outfile' and our tree in 'outtree', |
194 | # both in the temp directory. |
195 | |
196 | my @outtree; |
197 | if( -f "$phylip_dir/outtree" ) { |
198 | open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read"; |
199 | @outtree = <TREE>; |
200 | close TREE; |
201 | } |
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202 | return join( '', @outtree ) if @outtree; |
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203 | |
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204 | # If we got this far, we are about to throw an error. |
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205 | my @error; |
206 | if( -f "$phylip_dir/outfile" ) { |
207 | open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read"; |
208 | @error = <OUTPUT>; |
209 | close OUTPUT; |
210 | } else { |
211 | push( @error, "Neither outtree nor output file was produced!" ); |
212 | } |
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213 | throw( join( '', @error ) ); |
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214 | } |
215 | |
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216 | =head2 parse_newick( $newick_string ) |
217 | |
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218 | Parses the given Newick tree(s) into one or more Stemma objects with |
219 | undirected graphs. |
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220 | |
221 | =cut |
222 | |
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223 | sub parse_newick { |
224 | my $newick = shift; |
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225 | my @stemmata; |
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226 | # Parse the result into a tree |
227 | my $forest = Bio::Phylo::IO->parse( |
228 | -format => 'newick', |
229 | -string => $newick, |
230 | ); |
231 | # Turn the tree into a graph, starting with the root node |
232 | foreach my $tree ( @{$forest->get_entities} ) { |
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233 | my $stemma = Text::Tradition::Stemma->new( |
234 | graph => _graph_from_bio( $tree ), |
235 | is_undirected => 1 ); |
236 | push( @stemmata, $stemma ); |
237 | } |
238 | return \@stemmata; |
239 | } |
240 | |
241 | sub _graph_from_bio { |
242 | my $tree = shift; |
243 | my $graph = Graph->new( 'undirected' => 1 ); |
244 | # Give all the intermediate anonymous nodes a name. |
245 | my $i = 0; |
246 | my $classes = {}; |
247 | foreach my $n ( @{$tree->get_terminals} ) { |
248 | # The terminal nodes are our named witnesses. |
249 | $classes->{$n->get_name} = 'extant'; |
250 | } |
251 | foreach my $n ( @{$tree->get_internals} ) { |
252 | unless( defined $n->get_name && $n->get_name ne '' ) { |
253 | # Get an integer, make sure it's a unique name |
254 | while( exists $classes->{$i} ) { |
255 | $i++; |
256 | } |
257 | $n->set_name( $i++ ); |
258 | } |
259 | $classes->{$n->get_name} = 'hypothetical'; |
260 | } |
261 | _add_tree_children( $graph, $classes, undef, [ $tree->get_root ]); |
262 | return $graph; |
263 | } |
264 | |
265 | sub _add_tree_children { |
266 | my( $graph, $classes, $parent, $tree_children ) = @_; |
267 | foreach my $c ( @$tree_children ) { |
268 | my $child = $c->get_name; |
269 | $graph->add_vertex( $child ); |
270 | $graph->set_vertex_attribute( $child, 'class', $classes->{$child} ); |
271 | $graph->add_path( $parent, $child ) if defined $parent; |
272 | _add_tree_children( $graph, $classes, $child, $c->get_children() ); |
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273 | } |
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274 | } |
275 | |
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276 | =head2 newick_to_svg( $newick_string ) |
277 | |
278 | Uses the FigTree utility (if installed) to transform the given Newick tree(s) |
279 | into a graph visualization. |
280 | |
281 | =cut |
282 | |
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283 | sub newick_to_svg { |
284 | my $newick = shift; |
285 | my $program = File::Which::which( 'figtree' ); |
286 | unless( -x $program ) { |
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287 | throw( "FigTree commandline utility not found in path" ); |
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288 | } |
289 | my $svg; |
290 | my $nfile = File::Temp->new(); |
291 | print $nfile $newick; |
292 | close $nfile; |
293 | my @cmd = ( $program, '-graphic', 'SVG', $nfile ); |
294 | run( \@cmd, ">", binary(), \$svg ); |
295 | return decode_utf8( $svg ); |
296 | } |
297 | |
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298 | sub throw { |
299 | Text::Tradition::Error->throw( |
300 | 'ident' => 'StemmaUtil error', |
301 | 'message' => $_[0], |
302 | ); |
303 | } |
304 | |
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305 | 1; |
306 | |
307 | =head1 LICENSE |
308 | |
309 | This package is free software and is provided "as is" without express |
310 | or implied warranty. You can redistribute it and/or modify it under |
311 | the same terms as Perl itself. |
312 | |
313 | =head1 AUTHOR |
314 | |
315 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |