Commit | Line | Data |
68454b71 |
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; |
8 | use File::chdir; |
9 | use File::Temp; |
10 | use File::Which; |
11 | use Graph; |
12 | use Graph::Reader::Dot; |
13 | use IPC::Run qw/ run binary /; |
14 | @EXPORT_OK = qw/ make_character_matrix character_input phylip_pars parse_newick /; |
68454b71 |
15 | |
16 | sub make_character_matrix { |
17 | my( $table ) = @_; |
18 | # Push the names of the witnesses to initialize the rows of the matrix. |
19 | my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] } |
20 | @{$table->{'alignment'}}; |
21 | foreach my $token_index ( 0 .. $table->{'length'} - 1) { |
22 | # First implementation: make dumb alignment table, caring about |
23 | # nothing except which reading is in which position. |
24 | my @pos_readings = map { $_->{'tokens'}->[$token_index] } |
25 | @{$table->{'alignment'}}; |
26 | my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings; |
27 | my @chars = convert_characters( \@pos_text ); |
28 | foreach my $idx ( 0 .. $#matrix ) { |
29 | push( @{$matrix[$idx]}, $chars[$idx] ); |
30 | } |
31 | } |
32 | return \@matrix; |
33 | } |
34 | |
35 | # Helper function to make the witness name something legal for pars |
36 | |
37 | sub _normalize_witname { |
38 | my( $witname ) = @_; |
39 | $witname =~ s/\s+/ /g; |
40 | $witname =~ s/[\[\]\(\)\:;,]//g; |
41 | $witname = substr( $witname, 0, 10 ); |
42 | return sprintf( "%-10s", $witname ); |
43 | } |
44 | |
45 | sub convert_characters { |
46 | my $row = shift; |
47 | # This is a simple algorithm that treats every reading as different. |
48 | # Eventually we will want to be able to specify how relationships |
49 | # affect the character matrix. |
50 | my %unique = ( '__UNDEF__' => 'X', |
51 | '#LACUNA#' => '?', |
52 | ); |
53 | my %count; |
54 | my $ctr = 0; |
55 | foreach my $word ( @$row ) { |
56 | if( $word && !exists $unique{$word} ) { |
57 | $unique{$word} = chr( 65 + $ctr ); |
58 | $ctr++; |
59 | } |
60 | $count{$word}++ if $word; |
61 | } |
62 | # Try to keep variants under 8 by lacunizing any singletons. |
63 | if( scalar( keys %unique ) > 8 ) { |
64 | foreach my $word ( keys %count ) { |
65 | if( $count{$word} == 1 ) { |
66 | $unique{$word} = '?'; |
67 | } |
68 | } |
69 | } |
70 | my %u = reverse %unique; |
71 | if( scalar( keys %u ) > 8 ) { |
72 | warn "Have more than 8 variants on this location; phylip will break"; |
73 | } |
74 | my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row; |
75 | return @chars; |
76 | } |
77 | |
b02332ca |
78 | sub character_input { |
68454b71 |
79 | my $table = shift; |
80 | my $character_matrix = make_character_matrix( $table ); |
81 | my $input = ''; |
82 | my $rows = scalar @{$character_matrix}; |
83 | my $columns = scalar @{$character_matrix->[0]} - 1; |
84 | $input .= "\t$rows\t$columns\n"; |
85 | foreach my $row ( @{$character_matrix} ) { |
86 | $input .= join( '', @$row ) . "\n"; |
87 | } |
88 | return $input; |
89 | } |
90 | |
b02332ca |
91 | sub phylip_pars { |
92 | my( $charmatrix ) = @_; |
93 | # Set up a temporary directory for all the default Phylip files. |
94 | my $phylip_dir = File::Temp->newdir(); |
95 | # $phylip_dir->unlink_on_destroy(0); |
96 | # We need an infile, and we need a command input file. |
97 | open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile"; |
98 | print MATRIX $charmatrix; |
99 | close MATRIX; |
100 | |
101 | open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile"; |
102 | ## TODO any configuration parameters we want to set here |
103 | # U Search for best tree? Yes |
104 | # S Search option? More thorough search |
105 | # V Number of trees to save? 100 |
106 | # J Randomize input order of species? No. Use input order |
107 | # O Outgroup root? No, use as outgroup species 1 |
108 | # T Use Threshold parsimony? No, use ordinary parsimony |
109 | # W Sites weighted? No |
110 | # M Analyze multiple data sets? No |
111 | # I Input species interleaved? Yes |
112 | # 0 Terminal type (IBM PC, ANSI, none)? ANSI |
113 | # 1 Print out the data at start of run No |
114 | # 2 Print indications of progress of run Yes |
115 | # 3 Print out tree Yes |
116 | # 4 Print out steps in each site No |
117 | # 5 Print character at all nodes of tree No |
118 | # 6 Write out trees onto tree file? Yes |
119 | print CMD "Y\n"; |
120 | close CMD; |
121 | |
122 | # And then we run the program. |
123 | my $program = File::Which::which( 'pars' ); |
124 | unless( -x $program ) { |
125 | return( undef, "Phylip pars not found in path" ); |
126 | } |
127 | |
128 | { |
129 | # We need to run it in our temporary directory where we have created |
130 | # all the expected files. |
131 | local $CWD = $phylip_dir; |
132 | my @cmd = ( $program ); |
133 | run \@cmd, '<', 'cmdfile', '>', '/dev/null'; |
134 | } |
135 | # Now our output should be in 'outfile' and our tree in 'outtree', |
136 | # both in the temp directory. |
137 | |
138 | my @outtree; |
139 | if( -f "$phylip_dir/outtree" ) { |
140 | open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read"; |
141 | @outtree = <TREE>; |
142 | close TREE; |
143 | } |
144 | return( 1, join( '', @outtree ) ) if @outtree; |
145 | |
146 | my @error; |
147 | if( -f "$phylip_dir/outfile" ) { |
148 | open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read"; |
149 | @error = <OUTPUT>; |
150 | close OUTPUT; |
151 | } else { |
152 | push( @error, "Neither outtree nor output file was produced!" ); |
153 | } |
154 | return( undef, join( '', @error ) ); |
155 | } |
156 | |
157 | sub parse_newick { |
158 | my $newick = shift; |
159 | my @trees; |
160 | # Parse the result into a tree |
161 | my $forest = Bio::Phylo::IO->parse( |
162 | -format => 'newick', |
163 | -string => $newick, |
164 | ); |
165 | # Turn the tree into a graph, starting with the root node |
166 | foreach my $tree ( @{$forest->get_entities} ) { |
167 | push( @trees, _graph_from_bio( $tree ) ); |
168 | } |
169 | return \@trees; |
170 | } |
171 | |
172 | sub _graph_from_bio { |
173 | my $tree = shift; |
174 | my $graph = Graph->new( 'undirected' => 1 ); |
175 | # Give all the intermediate anonymous nodes a name. |
176 | my $i = 0; |
177 | foreach my $n ( @{$tree->get_entities} ) { |
178 | next if $n->get_name; |
179 | $n->set_name( $i++ ); |
180 | } |
181 | my $root = $tree->get_root->get_name; |
182 | $graph->add_vertex( $root ); |
183 | _add_tree_children( $graph, $root, $tree->get_root->get_children() ); |
184 | return $graph; |
185 | } |
186 | |
187 | sub _add_tree_children { |
188 | my( $graph, $parent, $tree_children ) = @_; |
189 | foreach my $c ( @$tree_children ) { |
190 | my $child = $c->get_name; |
191 | $graph->add_vertex( $child ); |
192 | $graph->add_path( $parent, $child ); |
193 | _add_tree_children( $graph, $child, $c->get_children() ); |
194 | } |
195 | } |