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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 ) { |
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25 | warn "Need a linear graph in order to make an alignment table"; |
26 | return; |
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27 | } |
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28 | my $table = $self->collation->make_alignment_table; |
29 | # Push the names of the witnesses to initialize the rows of the matrix. |
30 | my @matrix = map { [ $self->_normalize_ac( $_ ) ] } @{$table->[0]}; |
31 | $DB::single = 1; |
32 | foreach my $token_index ( 1 .. $#{$table} ) { |
33 | # First implementation: make dumb alignment table, caring about |
34 | # nothing except which reading is in which position. |
35 | my @chars = convert_characters( $table->[$token_index] ); |
36 | foreach my $idx ( 0 .. $#matrix ) { |
37 | push( @{$matrix[$idx]}, $chars[$idx] ); |
38 | } |
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39 | } |
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40 | $self->_save_character_matrix( \@matrix ); |
41 | } |
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42 | |
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43 | sub _normalize_ac { |
44 | my( $self, $witname ) = @_; |
45 | my $ac = $self->collation->ac_label; |
46 | if( $witname =~ /(.*)\Q$ac\E$/ ) { |
47 | $witname = $1 . '_ac'; |
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48 | } |
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49 | return sprintf( "%-10s", $witname ); |
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50 | } |
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51 | |
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52 | sub convert_characters { |
53 | my $row = shift; |
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54 | # This is a simple algorithm that treats every reading as different. |
55 | # Eventually we will want to be able to specify how relationships |
56 | # affect the character matrix. |
eca16057 |
57 | my %unique = ( '__UNDEF__' => 'X', |
58 | '#LACUNA#' => '?', |
59 | ); |
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60 | my $ctr = 0; |
61 | foreach my $word ( @$row ) { |
62 | if( $word && !exists $unique{$word} ) { |
63 | $unique{$word} = chr( 65 + $ctr ); |
64 | $ctr++; |
65 | } |
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66 | } |
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67 | if( scalar( keys %unique ) > 8 ) { |
68 | warn "Have more than 8 variants on this location; pars will break"; |
69 | } |
70 | my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row; |
71 | return @chars; |
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72 | } |
73 | |
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74 | sub pars_input { |
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75 | my $self = shift; |
76 | $self->make_character_matrix unless $self->has_character_matrix; |
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77 | my $matrix = ''; |
78 | my $rows = scalar @{$self->character_matrix}; |
79 | my $columns = scalar @{$self->character_matrix->[0]} - 1; |
80 | $matrix .= "\t$rows\t$columns\n"; |
81 | foreach my $row ( @{$self->character_matrix} ) { |
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82 | $matrix .= join( '', @$row ) . "\n"; |
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83 | } |
84 | return $matrix; |
85 | } |
86 | |
87 | sub run_pars { |
88 | my $self = shift; |
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89 | |
90 | # Set up a temporary directory for all the default Phylip files. |
91 | my $phylip_dir = File::Temp->newdir(); |
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92 | print STDERR $phylip_dir . "\n"; |
93 | # $phylip_dir->unlink_on_destroy(0); |
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94 | # We need an infile, and we need a command input file. |
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95 | open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile"; |
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96 | print MATRIX $self->pars_input(); |
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97 | close MATRIX; |
98 | |
99 | open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile"; |
100 | ## TODO any configuration parameters we want to set here |
101 | # U Search for best tree? Yes |
102 | # S Search option? More thorough search |
103 | # V Number of trees to save? 100 |
104 | # J Randomize input order of species? No. Use input order |
105 | # O Outgroup root? No, use as outgroup species 1 |
106 | # T Use Threshold parsimony? No, use ordinary parsimony |
107 | # W Sites weighted? No |
108 | # M Analyze multiple data sets? No |
109 | # I Input species interleaved? Yes |
110 | # 0 Terminal type (IBM PC, ANSI, none)? ANSI |
111 | # 1 Print out the data at start of run No |
112 | # 2 Print indications of progress of run Yes |
113 | # 3 Print out tree Yes |
114 | # 4 Print out steps in each site No |
115 | # 5 Print character at all nodes of tree No |
116 | # 6 Write out trees onto tree file? Yes |
117 | print CMD "Y\n"; |
118 | close CMD; |
119 | |
120 | # And then we run the program. |
121 | ### HACKY HACKY |
122 | my $PHYLIP_PATH = '/Users/tla/Projects/phylip-3.69/exe'; |
123 | my $program = "pars"; |
124 | if( $^O eq 'darwin' ) { |
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125 | $program = "$PHYLIP_PATH/$program.app/Contents/MacOS/$program"; |
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126 | } else { |
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127 | $program = "$PHYLIP_PATH/$program"; |
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128 | } |
129 | |
130 | { |
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131 | # We need to run it in our temporary directory where we have created |
132 | # all the expected files. |
133 | local $CWD = $phylip_dir; |
134 | my @cmd = ( $program ); |
135 | run \@cmd, '<', 'cmdfile', '>', '/dev/null'; |
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136 | } |
137 | # Now our output should be in 'outfile' and our tree in 'outtree', |
138 | # both in the temp directory. |
139 | |
140 | my @outtree; |
141 | if( -f "$phylip_dir/outtree" ) { |
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142 | open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read"; |
143 | @outtree = <TREE>; |
144 | close TREE; |
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145 | } |
146 | return( 1, join( '', @outtree ) ) if @outtree; |
147 | |
148 | my @error; |
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149 | if( -f "$phylip_dir/outfile" ) { |
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150 | open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read"; |
151 | @error = <OUTPUT>; |
152 | close OUTPUT; |
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153 | } else { |
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154 | push( @error, "Neither outtree nor output file was produced!" ); |
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155 | } |
156 | return( undef, join( '', @error ) ); |
157 | } |
158 | |
159 | no Moose; |
160 | __PACKAGE__->meta->make_immutable; |
161 | |
162 | 1; |