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1 | package Text::Tradition::Stemma; |
2 | |
3 | use File::chdir; |
4 | use File::Temp; |
5 | use IPC::Run qw/ run /; |
6 | use Moose; |
7 | use Text::Tradition::Collation::Position; |
8 | |
9 | has collation => ( |
10 | is => 'ro', |
11 | isa => 'Text::Tradition::Collation', |
12 | required => 1, |
13 | ); |
14 | |
15 | has character_matrix => ( |
16 | is => 'ro', |
17 | isa => 'ArrayRef[ArrayRef[Str]]', |
18 | writer => '_save_character_matrix', |
19 | predicate => 'has_character_matrix', |
20 | ); |
21 | |
22 | sub make_character_matrix { |
23 | my $self = shift; |
24 | unless( $self->collation->linear ) { |
25 | warn "Need a linear graph in order to make an alignment table"; |
26 | return; |
27 | } |
28 | my @all_pos = sort { Text::Tradition::Collation::Position::str_cmp( $a, $b ) } |
29 | $self->collation->possible_positions; |
30 | my $table = []; |
31 | my $characters = {}; |
32 | map { $characters->{$_} = {} } @all_pos; |
33 | foreach my $wit ( @{$self->collation->tradition->witnesses} ) { |
34 | # First implementation: make dumb alignment table, caring about |
35 | # nothing except which reading is in which position. |
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36 | my $sigilfield = sprintf( "%-10s", $wit->sigil ); |
37 | push( @$table, [ $sigilfield, make_witness_row( $characters, $wit->path, |
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38 | \@all_pos ) ] ); |
39 | if( $wit->has_ante_corr ) { |
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40 | $sigilfield = sprintf( "%-10s", $wit->sigil . "_ac" ); |
41 | push( @$table, [ $sigilfield, |
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42 | make_witness_row( $characters, $wit->uncorrected_path, |
43 | \@all_pos ) ] ); |
44 | } |
45 | } |
46 | $self->_save_character_matrix( $table ); |
47 | } |
48 | |
49 | sub make_witness_row { |
50 | my( $characters, $path, $positions ) = @_; |
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51 | my %char_hash; |
52 | map { $char_hash{$_} = 'X' } @$positions; |
53 | foreach my $rdg( @$path ) { |
54 | $char_hash{$rdg->position->minref} = get_character( $rdg, $characters ); |
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55 | } |
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56 | my @row = map { $char_hash{$_} } @$positions; |
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57 | return @row; |
58 | } |
59 | |
60 | |
61 | sub get_character { |
62 | my( $reading, $characters ) = @_; |
63 | my $this_pos = $characters->{$reading->position->minref}; |
64 | # This is a simple algorithm that treats every reading as different. |
65 | # Eventually we will want to be able to specify how relationships |
66 | # affect the character matrix. |
67 | my $text = $reading->text; |
68 | unless( exists $this_pos->{$text} ) { |
69 | # We need to find what the next character is here, and record it. |
70 | my @all_chr = sort { $a <=> $b } values( %$this_pos ); |
71 | if( @all_chr == 8 ) { |
72 | warn "Already have eight variants at position " |
73 | . $reading->position->minref . "; not adding " . $reading->text; |
74 | return '?'; |
75 | } |
76 | $this_pos->{$text} = scalar @all_chr; |
77 | } |
78 | return $this_pos->{$text}; |
79 | } |
80 | |
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81 | sub pars_input { |
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82 | my $self = shift; |
83 | $self->make_character_matrix unless $self->has_character_matrix; |
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84 | my $matrix = ''; |
85 | my $rows = scalar @{$self->character_matrix}; |
86 | my $columns = scalar @{$self->character_matrix->[0]} - 1; |
87 | $matrix .= "\t$rows\t$columns\n"; |
88 | foreach my $row ( @{$self->character_matrix} ) { |
89 | $matrix .= join( '', @$row ) . "\n"; |
90 | } |
91 | return $matrix; |
92 | } |
93 | |
94 | sub run_pars { |
95 | my $self = shift; |
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96 | |
97 | # Set up a temporary directory for all the default Phylip files. |
98 | my $phylip_dir = File::Temp->newdir(); |
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99 | $DB::single = 1; |
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100 | # We need an infile, and we need a command input file. |
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101 | open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile"; |
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102 | print MATRIX $self->pars_input(); |
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103 | close MATRIX; |
104 | |
105 | open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile"; |
106 | ## TODO any configuration parameters we want to set here |
107 | # U Search for best tree? Yes |
108 | # S Search option? More thorough search |
109 | # V Number of trees to save? 100 |
110 | # J Randomize input order of species? No. Use input order |
111 | # O Outgroup root? No, use as outgroup species 1 |
112 | # T Use Threshold parsimony? No, use ordinary parsimony |
113 | # W Sites weighted? No |
114 | # M Analyze multiple data sets? No |
115 | # I Input species interleaved? Yes |
116 | # 0 Terminal type (IBM PC, ANSI, none)? ANSI |
117 | # 1 Print out the data at start of run No |
118 | # 2 Print indications of progress of run Yes |
119 | # 3 Print out tree Yes |
120 | # 4 Print out steps in each site No |
121 | # 5 Print character at all nodes of tree No |
122 | # 6 Write out trees onto tree file? Yes |
123 | print CMD "Y\n"; |
124 | close CMD; |
125 | |
126 | # And then we run the program. |
127 | ### HACKY HACKY |
128 | my $PHYLIP_PATH = '/Users/tla/Projects/phylip-3.69/exe'; |
129 | my $program = "pars"; |
130 | if( $^O eq 'darwin' ) { |
131 | $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program"; |
132 | } else { |
133 | $program = "$PHYLIP_PATH/$program"; |
134 | } |
135 | |
136 | { |
137 | # We need to run it in our temporary directory where we have created |
138 | # all the expected files. |
139 | local $CWD = $phylip_dir; |
140 | my @cmd = ( $program ); |
141 | run \@cmd, '<', 'cmdfile', '>', '/dev/null'; |
142 | } |
143 | # Now our output should be in 'outfile' and our tree in 'outtree', |
144 | # both in the temp directory. |
145 | |
146 | my @outtree; |
147 | if( -f "$phylip_dir/outtree" ) { |
148 | open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read"; |
149 | @outtree = <TREE>; |
150 | close TREE; |
151 | } |
152 | return( 1, join( '', @outtree ) ) if @outtree; |
153 | |
154 | my @error; |
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155 | if( -f "$phylip_dir/outfile" ) { |
156 | open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read"; |
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157 | @error = <OUTPUT>; |
158 | close OUTPUT; |
159 | } else { |
160 | push( @error, "Neither outtree nor output file was produced!" ); |
161 | } |
162 | return( undef, join( '', @error ) ); |
163 | } |
164 | |
165 | no Moose; |
166 | __PACKAGE__->meta->make_immutable; |
167 | |
168 | 1; |