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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; |
13 | use Graph::Reader::Dot; |
14 | use IPC::Run qw/ run binary /; |
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15 | use Text::Tradition::Error; |
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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( $alignment_table ) |
30 | |
31 | Returns a character matrix string suitable for Phylip programs, which |
32 | corresponds to the given alignment table. See Text::Tradition::Collation |
33 | for a description of the alignment table format. |
34 | |
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35 | =cut |
36 | |
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37 | sub character_input { |
38 | my $table = shift; |
39 | my $character_matrix = _make_character_matrix( $table ); |
40 | my $input = ''; |
41 | my $rows = scalar @{$character_matrix}; |
42 | my $columns = scalar @{$character_matrix->[0]} - 1; |
43 | $input .= "\t$rows\t$columns\n"; |
44 | foreach my $row ( @{$character_matrix} ) { |
45 | $input .= join( '', @$row ) . "\n"; |
46 | } |
47 | return $input; |
48 | } |
49 | |
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50 | sub _make_character_matrix { |
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51 | my( $table ) = @_; |
52 | # Push the names of the witnesses to initialize the rows of the matrix. |
53 | my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] } |
54 | @{$table->{'alignment'}}; |
55 | foreach my $token_index ( 0 .. $table->{'length'} - 1) { |
56 | # First implementation: make dumb alignment table, caring about |
57 | # nothing except which reading is in which position. |
58 | my @pos_readings = map { $_->{'tokens'}->[$token_index] } |
59 | @{$table->{'alignment'}}; |
60 | my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings; |
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61 | my @chars = _convert_characters( \@pos_text ); |
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62 | foreach my $idx ( 0 .. $#matrix ) { |
63 | push( @{$matrix[$idx]}, $chars[$idx] ); |
64 | } |
65 | } |
66 | return \@matrix; |
67 | } |
68 | |
69 | # Helper function to make the witness name something legal for pars |
70 | |
71 | sub _normalize_witname { |
72 | my( $witname ) = @_; |
73 | $witname =~ s/\s+/ /g; |
74 | $witname =~ s/[\[\]\(\)\:;,]//g; |
75 | $witname = substr( $witname, 0, 10 ); |
76 | return sprintf( "%-10s", $witname ); |
77 | } |
78 | |
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79 | sub _convert_characters { |
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80 | my $row = shift; |
81 | # This is a simple algorithm that treats every reading as different. |
82 | # Eventually we will want to be able to specify how relationships |
83 | # affect the character matrix. |
84 | my %unique = ( '__UNDEF__' => 'X', |
85 | '#LACUNA#' => '?', |
86 | ); |
87 | my %count; |
88 | my $ctr = 0; |
89 | foreach my $word ( @$row ) { |
90 | if( $word && !exists $unique{$word} ) { |
91 | $unique{$word} = chr( 65 + $ctr ); |
92 | $ctr++; |
93 | } |
94 | $count{$word}++ if $word; |
95 | } |
96 | # Try to keep variants under 8 by lacunizing any singletons. |
97 | if( scalar( keys %unique ) > 8 ) { |
98 | foreach my $word ( keys %count ) { |
99 | if( $count{$word} == 1 ) { |
100 | $unique{$word} = '?'; |
101 | } |
102 | } |
103 | } |
104 | my %u = reverse %unique; |
105 | if( scalar( keys %u ) > 8 ) { |
106 | warn "Have more than 8 variants on this location; phylip will break"; |
107 | } |
108 | my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row; |
109 | return @chars; |
110 | } |
111 | |
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112 | =head2 phylip_pars( $character_matrix ) |
113 | |
114 | Runs Phylip Pars on the given character matrix. Returns results in Newick format. |
115 | |
116 | =cut |
117 | |
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118 | sub phylip_pars { |
119 | my( $charmatrix ) = @_; |
120 | # Set up a temporary directory for all the default Phylip files. |
121 | my $phylip_dir = File::Temp->newdir(); |
122 | # $phylip_dir->unlink_on_destroy(0); |
123 | # We need an infile, and we need a command input file. |
124 | open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile"; |
125 | print MATRIX $charmatrix; |
126 | close MATRIX; |
127 | |
128 | open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile"; |
129 | ## TODO any configuration parameters we want to set here |
130 | # U Search for best tree? Yes |
131 | # S Search option? More thorough search |
132 | # V Number of trees to save? 100 |
133 | # J Randomize input order of species? No. Use input order |
134 | # O Outgroup root? No, use as outgroup species 1 |
135 | # T Use Threshold parsimony? No, use ordinary parsimony |
136 | # W Sites weighted? No |
137 | # M Analyze multiple data sets? No |
138 | # I Input species interleaved? Yes |
139 | # 0 Terminal type (IBM PC, ANSI, none)? ANSI |
140 | # 1 Print out the data at start of run No |
141 | # 2 Print indications of progress of run Yes |
142 | # 3 Print out tree Yes |
143 | # 4 Print out steps in each site No |
144 | # 5 Print character at all nodes of tree No |
145 | # 6 Write out trees onto tree file? Yes |
146 | print CMD "Y\n"; |
147 | close CMD; |
148 | |
149 | # And then we run the program. |
150 | my $program = File::Which::which( 'pars' ); |
151 | unless( -x $program ) { |
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152 | throw( "Phylip pars not found in path" ); |
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153 | } |
154 | |
155 | { |
156 | # We need to run it in our temporary directory where we have created |
157 | # all the expected files. |
158 | local $CWD = $phylip_dir; |
159 | my @cmd = ( $program ); |
160 | run \@cmd, '<', 'cmdfile', '>', '/dev/null'; |
161 | } |
162 | # Now our output should be in 'outfile' and our tree in 'outtree', |
163 | # both in the temp directory. |
164 | |
165 | my @outtree; |
166 | if( -f "$phylip_dir/outtree" ) { |
167 | open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read"; |
168 | @outtree = <TREE>; |
169 | close TREE; |
170 | } |
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171 | return join( '', @outtree ) if @outtree; |
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172 | |
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173 | # If we got this far, we are about to throw an error. |
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174 | my @error; |
175 | if( -f "$phylip_dir/outfile" ) { |
176 | open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read"; |
177 | @error = <OUTPUT>; |
178 | close OUTPUT; |
179 | } else { |
180 | push( @error, "Neither outtree nor output file was produced!" ); |
181 | } |
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182 | throw( join( '', @error ) ); |
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183 | } |
184 | |
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185 | =head2 parse_newick( $newick_string ) |
186 | |
187 | Parses the given Newick tree(s) into one or more undirected Graph objects. |
188 | |
189 | =cut |
190 | |
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191 | sub parse_newick { |
192 | my $newick = shift; |
193 | my @trees; |
194 | # Parse the result into a tree |
195 | my $forest = Bio::Phylo::IO->parse( |
196 | -format => 'newick', |
197 | -string => $newick, |
198 | ); |
199 | # Turn the tree into a graph, starting with the root node |
200 | foreach my $tree ( @{$forest->get_entities} ) { |
201 | push( @trees, _graph_from_bio( $tree ) ); |
202 | } |
203 | return \@trees; |
204 | } |
205 | |
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206 | =head2 newick_to_svg( $newick_string ) |
207 | |
208 | Uses the FigTree utility (if installed) to transform the given Newick tree(s) |
209 | into a graph visualization. |
210 | |
211 | =cut |
212 | |
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213 | sub newick_to_svg { |
214 | my $newick = shift; |
215 | my $program = File::Which::which( 'figtree' ); |
216 | unless( -x $program ) { |
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217 | throw( "FigTree commandline utility not found in path" ); |
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218 | } |
219 | my $svg; |
220 | my $nfile = File::Temp->new(); |
221 | print $nfile $newick; |
222 | close $nfile; |
223 | my @cmd = ( $program, '-graphic', 'SVG', $nfile ); |
224 | run( \@cmd, ">", binary(), \$svg ); |
225 | return decode_utf8( $svg ); |
226 | } |
227 | |
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228 | sub _graph_from_bio { |
229 | my $tree = shift; |
230 | my $graph = Graph->new( 'undirected' => 1 ); |
231 | # Give all the intermediate anonymous nodes a name. |
232 | my $i = 0; |
233 | foreach my $n ( @{$tree->get_entities} ) { |
234 | next if $n->get_name; |
235 | $n->set_name( $i++ ); |
236 | } |
237 | my $root = $tree->get_root->get_name; |
238 | $graph->add_vertex( $root ); |
239 | _add_tree_children( $graph, $root, $tree->get_root->get_children() ); |
240 | return $graph; |
241 | } |
242 | |
243 | sub _add_tree_children { |
244 | my( $graph, $parent, $tree_children ) = @_; |
245 | foreach my $c ( @$tree_children ) { |
246 | my $child = $c->get_name; |
247 | $graph->add_vertex( $child ); |
248 | $graph->add_path( $parent, $child ); |
249 | _add_tree_children( $graph, $child, $c->get_children() ); |
250 | } |
251 | } |
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252 | |
253 | sub throw { |
254 | Text::Tradition::Error->throw( |
255 | 'ident' => 'StemmaUtil error', |
256 | 'message' => $_[0], |
257 | ); |
258 | } |
259 | |
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260 | 1; |
261 | |
262 | =head1 LICENSE |
263 | |
264 | This package is free software and is provided "as is" without express |
265 | or implied warranty. You can redistribute it and/or modify it under |
266 | the same terms as Perl itself. |
267 | |
268 | =head1 AUTHOR |
269 | |
270 | Tara L Andrews E<lt>aurum@cpan.orgE<gt> |