Commit | Line | Data |
9463b0bf |
1 | package Text::Tradition::Stemma; |
2 | |
40f19742 |
3 | use Bio::Phylo::IO; |
e79c23c7 |
4 | use Encode qw( decode_utf8 ); |
9463b0bf |
5 | use File::chdir; |
6 | use File::Temp; |
e05997e2 |
7 | use Graph; |
e79c23c7 |
8 | use Graph::Convert; |
e05997e2 |
9 | use Graph::Reader::Dot; |
e79c23c7 |
10 | use IPC::Run qw/ run binary /; |
40f19742 |
11 | use Moose; |
12 | use Text::Balanced qw/ extract_bracketed /; |
9463b0bf |
13 | |
14 | has collation => ( |
15 | is => 'ro', |
16 | isa => 'Text::Tradition::Collation', |
17 | required => 1, |
8d9a1cd8 |
18 | weak_ref => 1, |
9463b0bf |
19 | ); |
20 | |
e05997e2 |
21 | has graph => ( |
22 | is => 'rw', |
23 | isa => 'Graph', |
24 | predicate => 'has_graph', |
25 | ); |
26 | |
40f19742 |
27 | has distance_trees => ( |
28 | is => 'ro', |
29 | isa => 'ArrayRef[Graph]', |
30 | writer => '_save_distance_trees', |
31 | predicate => 'has_distance_trees', |
32 | ); |
c0ccdb62 |
33 | |
e05997e2 |
34 | sub BUILD { |
35 | my( $self, $args ) = @_; |
36 | # If we have been handed a dotfile, initialize it into a graph. |
37 | if( exists $args->{'dot'} ) { |
8d9a1cd8 |
38 | $self->graph_from_dot( $args->{'dot'} ); |
e05997e2 |
39 | } |
c0ccdb62 |
40 | } |
41 | |
8d9a1cd8 |
42 | sub graph_from_dot { |
43 | my( $self, $dotfh ) = @_; |
44 | # Assume utf-8 |
45 | binmode( $dotfh, ':utf8' ); |
46 | my $reader = Graph::Reader::Dot->new(); |
47 | my $graph = $reader->read_graph( $dotfh ); |
48 | $graph |
49 | ? $self->graph( $graph ) |
50 | : warn "Failed to parse dot in $dotfh"; |
51 | } |
52 | |
53 | sub as_dot { |
e367f5c0 |
54 | my( $self, $opts ) = @_; |
e79c23c7 |
55 | # TODO add options for display, someday |
8d9a1cd8 |
56 | # TODO see what happens with Graph::Writer::Dot someday |
e79c23c7 |
57 | my $dgraph = Graph::Convert->as_graph_easy( $self->graph ); |
58 | # Set some class display attributes for 'hypothetical' and 'extant' nodes |
59 | $dgraph->set_attribute( 'flow', 'south' ); |
60 | foreach my $n ( $dgraph->nodes ) { |
61 | if( $n->attribute( 'class' ) eq 'hypothetical' ) { |
62 | $n->set_attribute( 'shape', 'point' ); |
63 | $n->set_attribute( 'pointshape', 'diamond' ); |
64 | } else { |
65 | $n->set_attribute( 'shape', 'ellipse' ); |
66 | } |
67 | } |
68 | |
69 | # Render to svg via graphviz |
e367f5c0 |
70 | my @lines = split( /\n/, $dgraph->as_graphviz() ); |
71 | # Add the size attribute |
72 | if( $opts->{'size'} ) { |
73 | my $sizeline = " graph [ size=\"" . $opts->{'size'} . "\" ]"; |
74 | splice( @lines, 1, 0, $sizeline ); |
75 | } |
8d9a1cd8 |
76 | return join( "\n", @lines ); |
77 | } |
78 | |
79 | |
80 | # Render the stemma as SVG. |
81 | sub as_svg { |
82 | my( $self, $opts ) = @_; |
83 | my $dot = $self->as_dot( $opts ); |
e79c23c7 |
84 | my @cmd = qw/dot -Tsvg/; |
85 | my( $svg, $err ); |
86 | my $dotfile = File::Temp->new(); |
87 | ## TODO REMOVE |
88 | # $dotfile->unlink_on_destroy(0); |
89 | binmode $dotfile, ':utf8'; |
8d9a1cd8 |
90 | print $dotfile $dot; |
e79c23c7 |
91 | push( @cmd, $dotfile->filename ); |
92 | run( \@cmd, ">", binary(), \$svg ); |
93 | $svg = decode_utf8( $svg ); |
94 | return $svg; |
95 | } |
96 | |
08e0fb85 |
97 | sub witnesses { |
98 | my $self = shift; |
99 | my @wits = grep { $self->graph->get_vertex_attribute( $_, 'class' ) eq 'extant' } |
100 | $self->graph->vertices; |
101 | return @wits; |
102 | } |
103 | |
e79c23c7 |
104 | #### Methods for calculating phylogenetic trees #### |
105 | |
40f19742 |
106 | before 'distance_trees' => sub { |
107 | my $self = shift; |
108 | my %args = @_; |
109 | # TODO allow specification of method for calculating distance tree |
110 | if( $args{'recalc'} || !$self->has_distance_trees ) { |
111 | # We need to make a tree before we can return it. |
112 | my( $ok, $result ) = $self->run_phylip_pars(); |
113 | if( $ok ) { |
c0ccdb62 |
114 | # Save the resulting trees |
115 | my $trees = _parse_newick( $result ); |
116 | $self->_save_distance_trees( $trees ); |
40f19742 |
117 | } else { |
c0ccdb62 |
118 | warn "Failed to calculate distance trees: $result"; |
40f19742 |
119 | } |
120 | } |
121 | }; |
e05997e2 |
122 | |
9463b0bf |
123 | sub make_character_matrix { |
124 | my $self = shift; |
125 | unless( $self->collation->linear ) { |
910a0a6d |
126 | warn "Need a linear graph in order to make an alignment table"; |
127 | return; |
9463b0bf |
128 | } |
910a0a6d |
129 | my $table = $self->collation->make_alignment_table; |
130 | # Push the names of the witnesses to initialize the rows of the matrix. |
131 | my @matrix = map { [ $self->_normalize_ac( $_ ) ] } @{$table->[0]}; |
910a0a6d |
132 | foreach my $token_index ( 1 .. $#{$table} ) { |
133 | # First implementation: make dumb alignment table, caring about |
134 | # nothing except which reading is in which position. |
135 | my @chars = convert_characters( $table->[$token_index] ); |
136 | foreach my $idx ( 0 .. $#matrix ) { |
137 | push( @{$matrix[$idx]}, $chars[$idx] ); |
138 | } |
9463b0bf |
139 | } |
c0ccdb62 |
140 | return \@matrix; |
910a0a6d |
141 | } |
9463b0bf |
142 | |
910a0a6d |
143 | sub _normalize_ac { |
144 | my( $self, $witname ) = @_; |
145 | my $ac = $self->collation->ac_label; |
146 | if( $witname =~ /(.*)\Q$ac\E$/ ) { |
147 | $witname = $1 . '_ac'; |
9463b0bf |
148 | } |
910a0a6d |
149 | return sprintf( "%-10s", $witname ); |
9463b0bf |
150 | } |
9463b0bf |
151 | |
910a0a6d |
152 | sub convert_characters { |
153 | my $row = shift; |
9463b0bf |
154 | # This is a simple algorithm that treats every reading as different. |
155 | # Eventually we will want to be able to specify how relationships |
156 | # affect the character matrix. |
eca16057 |
157 | my %unique = ( '__UNDEF__' => 'X', |
158 | '#LACUNA#' => '?', |
159 | ); |
a7fb3133 |
160 | my %count; |
910a0a6d |
161 | my $ctr = 0; |
162 | foreach my $word ( @$row ) { |
163 | if( $word && !exists $unique{$word} ) { |
164 | $unique{$word} = chr( 65 + $ctr ); |
165 | $ctr++; |
166 | } |
a7fb3133 |
167 | $count{$word}++ if $word; |
9463b0bf |
168 | } |
a7fb3133 |
169 | # Try to keep variants under 8 by lacunizing any singletons. |
910a0a6d |
170 | if( scalar( keys %unique ) > 8 ) { |
a7fb3133 |
171 | foreach my $word ( keys %count ) { |
172 | if( $count{$word} == 1 ) { |
173 | $unique{$word} = '?'; |
174 | } |
175 | } |
176 | } |
177 | my %u = reverse %unique; |
178 | if( scalar( keys %u ) > 8 ) { |
40f19742 |
179 | warn "Have more than 8 variants on this location; phylip will break"; |
910a0a6d |
180 | } |
181 | my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row; |
182 | return @chars; |
9463b0bf |
183 | } |
184 | |
40f19742 |
185 | sub phylip_pars_input { |
9463b0bf |
186 | my $self = shift; |
c0ccdb62 |
187 | my $character_matrix = $self->make_character_matrix; |
188 | my $input = ''; |
189 | my $rows = scalar @{$character_matrix}; |
190 | my $columns = scalar @{$character_matrix->[0]} - 1; |
191 | $input .= "\t$rows\t$columns\n"; |
192 | foreach my $row ( @{$character_matrix} ) { |
193 | $input .= join( '', @$row ) . "\n"; |
f6066bac |
194 | } |
c0ccdb62 |
195 | return $input; |
f6066bac |
196 | } |
197 | |
40f19742 |
198 | sub run_phylip_pars { |
f6066bac |
199 | my $self = shift; |
9463b0bf |
200 | |
201 | # Set up a temporary directory for all the default Phylip files. |
202 | my $phylip_dir = File::Temp->newdir(); |
eca16057 |
203 | # $phylip_dir->unlink_on_destroy(0); |
f6066bac |
204 | # We need an infile, and we need a command input file. |
9463b0bf |
205 | open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile"; |
40f19742 |
206 | print MATRIX $self->phylip_pars_input(); |
9463b0bf |
207 | close MATRIX; |
208 | |
209 | open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile"; |
210 | ## TODO any configuration parameters we want to set here |
211 | # U Search for best tree? Yes |
212 | # S Search option? More thorough search |
213 | # V Number of trees to save? 100 |
214 | # J Randomize input order of species? No. Use input order |
215 | # O Outgroup root? No, use as outgroup species 1 |
216 | # T Use Threshold parsimony? No, use ordinary parsimony |
217 | # W Sites weighted? No |
218 | # M Analyze multiple data sets? No |
219 | # I Input species interleaved? Yes |
220 | # 0 Terminal type (IBM PC, ANSI, none)? ANSI |
221 | # 1 Print out the data at start of run No |
222 | # 2 Print indications of progress of run Yes |
223 | # 3 Print out tree Yes |
224 | # 4 Print out steps in each site No |
225 | # 5 Print character at all nodes of tree No |
226 | # 6 Write out trees onto tree file? Yes |
227 | print CMD "Y\n"; |
228 | close CMD; |
229 | |
230 | # And then we run the program. |
231 | ### HACKY HACKY |
232 | my $PHYLIP_PATH = '/Users/tla/Projects/phylip-3.69/exe'; |
233 | my $program = "pars"; |
234 | if( $^O eq 'darwin' ) { |
910a0a6d |
235 | $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program"; |
9463b0bf |
236 | } else { |
910a0a6d |
237 | $program = "$PHYLIP_PATH/$program"; |
9463b0bf |
238 | } |
239 | |
240 | { |
910a0a6d |
241 | # We need to run it in our temporary directory where we have created |
242 | # all the expected files. |
243 | local $CWD = $phylip_dir; |
244 | my @cmd = ( $program ); |
245 | run \@cmd, '<', 'cmdfile', '>', '/dev/null'; |
9463b0bf |
246 | } |
247 | # Now our output should be in 'outfile' and our tree in 'outtree', |
248 | # both in the temp directory. |
249 | |
250 | my @outtree; |
251 | if( -f "$phylip_dir/outtree" ) { |
910a0a6d |
252 | open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read"; |
253 | @outtree = <TREE>; |
254 | close TREE; |
9463b0bf |
255 | } |
256 | return( 1, join( '', @outtree ) ) if @outtree; |
257 | |
258 | my @error; |
f6066bac |
259 | if( -f "$phylip_dir/outfile" ) { |
910a0a6d |
260 | open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read"; |
261 | @error = <OUTPUT>; |
262 | close OUTPUT; |
9463b0bf |
263 | } else { |
910a0a6d |
264 | push( @error, "Neither outtree nor output file was produced!" ); |
9463b0bf |
265 | } |
266 | return( undef, join( '', @error ) ); |
267 | } |
268 | |
40f19742 |
269 | sub _parse_newick { |
270 | my $newick = shift; |
271 | my @trees; |
272 | # Parse the result into a tree |
273 | my $forest = Bio::Phylo::IO->parse( |
274 | -format => 'newick', |
275 | -string => $newick, |
276 | ); |
277 | # Turn the tree into a graph, starting with the root node |
278 | foreach my $tree ( @{$forest->get_entities} ) { |
279 | push( @trees, _graph_from_bio( $tree ) ); |
280 | } |
281 | return \@trees; |
282 | } |
283 | |
284 | sub _graph_from_bio { |
285 | my $tree = shift; |
286 | my $graph = Graph->new( 'undirected' => 1 ); |
287 | # Give all the intermediate anonymous nodes a name. |
288 | my $i = 0; |
289 | foreach my $n ( @{$tree->get_entities} ) { |
290 | next if $n->get_name; |
291 | $n->set_name( $i++ ); |
292 | } |
293 | my $root = $tree->get_root->get_name; |
294 | $graph->add_vertex( $root ); |
295 | _add_tree_children( $graph, $root, $tree->get_root->get_children() ); |
296 | return $graph; |
297 | } |
298 | |
299 | sub _add_tree_children { |
300 | my( $graph, $parent, $tree_children ) = @_; |
301 | foreach my $c ( @$tree_children ) { |
302 | my $child = $c->get_name; |
303 | $graph->add_vertex( $child ); |
304 | $graph->add_path( $parent, $child ); |
305 | _add_tree_children( $graph, $child, $c->get_children() ); |
306 | } |
307 | } |
308 | |
9463b0bf |
309 | no Moose; |
310 | __PACKAGE__->meta->make_immutable; |
311 | |
312 | 1; |