use warnings;
use Exporter 'import';
use vars qw/ @EXPORT_OK /;
-@EXPORT_OK = qw/ phylip_pars_input /;
+use Bio::Phylo::IO;
+use Encode qw( decode_utf8 );
+use File::chdir;
+use File::Temp;
+use File::Which;
+use Graph;
+use Graph::Reader::Dot;
+use IPC::Run qw/ run binary /;
+use Text::Tradition::Error;
+@EXPORT_OK = qw/ make_character_matrix character_input phylip_pars
+ parse_newick newick_to_svg /;
-sub make_character_matrix {
+=head1 NAME
+
+Text::Tradition::StemmaUtil - standalone utilities for distance tree calculations
+
+=head1 DESCRIPTION
+
+This package contains a set of utilities for running phylogenetic analysis on
+text collations.
+
+=head1 SUBROUTINES
+
+=cut
+
+sub _make_character_matrix {
my( $table ) = @_;
# Push the names of the witnesses to initialize the rows of the matrix.
my @matrix = map { [ _normalize_witname( $_->{'witness'} ) ] }
my @pos_readings = map { $_->{'tokens'}->[$token_index] }
@{$table->{'alignment'}};
my @pos_text = map { $_ ? $_->{'t'} : $_ } @pos_readings;
- my @chars = convert_characters( \@pos_text );
+ my @chars = _convert_characters( \@pos_text );
foreach my $idx ( 0 .. $#matrix ) {
push( @{$matrix[$idx]}, $chars[$idx] );
}
return sprintf( "%-10s", $witname );
}
-sub convert_characters {
+sub _convert_characters {
my $row = shift;
# This is a simple algorithm that treats every reading as different.
# Eventually we will want to be able to specify how relationships
return @chars;
}
-sub phylip_pars_input {
+=head2 character_input( $alignment_table )
+
+Returns a character matrix string suitable for Phylip programs, which
+corresponds to the given alignment table. See Text::Tradition::Collation
+for a description of the alignment table format.
+
+=cut
+
+sub character_input {
my $table = shift;
- my $character_matrix = make_character_matrix( $table );
+ my $character_matrix = _make_character_matrix( $table );
my $input = '';
my $rows = scalar @{$character_matrix};
my $columns = scalar @{$character_matrix->[0]} - 1;
return $input;
}
+=head2 phylip_pars( $character_matrix )
+
+Runs Phylip Pars on the given character matrix. Returns results in Newick format.
+
+=cut
+
+sub phylip_pars {
+ my( $charmatrix ) = @_;
+ # Set up a temporary directory for all the default Phylip files.
+ my $phylip_dir = File::Temp->newdir();
+ # $phylip_dir->unlink_on_destroy(0);
+ # We need an infile, and we need a command input file.
+ open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
+ print MATRIX $charmatrix;
+ close MATRIX;
+
+ open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
+ ## TODO any configuration parameters we want to set here
+# U Search for best tree? Yes
+# S Search option? More thorough search
+# V Number of trees to save? 100
+# J Randomize input order of species? No. Use input order
+# O Outgroup root? No, use as outgroup species 1
+# T Use Threshold parsimony? No, use ordinary parsimony
+# W Sites weighted? No
+# M Analyze multiple data sets? No
+# I Input species interleaved? Yes
+# 0 Terminal type (IBM PC, ANSI, none)? ANSI
+# 1 Print out the data at start of run No
+# 2 Print indications of progress of run Yes
+# 3 Print out tree Yes
+# 4 Print out steps in each site No
+# 5 Print character at all nodes of tree No
+# 6 Write out trees onto tree file? Yes
+ print CMD "Y\n";
+ close CMD;
+
+ # And then we run the program.
+ my $program = File::Which::which( 'pars' );
+ unless( -x $program ) {
+ throw( "Phylip pars not found in path" );
+ }
+
+ {
+ # We need to run it in our temporary directory where we have created
+ # all the expected files.
+ local $CWD = $phylip_dir;
+ my @cmd = ( $program );
+ run \@cmd, '<', 'cmdfile', '>', '/dev/null';
+ }
+ # Now our output should be in 'outfile' and our tree in 'outtree',
+ # both in the temp directory.
+
+ my @outtree;
+ if( -f "$phylip_dir/outtree" ) {
+ open( TREE, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
+ @outtree = <TREE>;
+ close TREE;
+ }
+ return join( '', @outtree ) if @outtree;
+
+ # If we got this far, we are about to throw an error.
+ my @error;
+ if( -f "$phylip_dir/outfile" ) {
+ open( OUTPUT, "$phylip_dir/outfile" ) or die "Could not open output for read";
+ @error = <OUTPUT>;
+ close OUTPUT;
+ } else {
+ push( @error, "Neither outtree nor output file was produced!" );
+ }
+ throw( join( '', @error ) );
+}
+
+=head2 parse_newick( $newick_string )
+
+Parses the given Newick tree(s) into one or more undirected Graph objects.
+
+=cut
+
+sub parse_newick {
+ my $newick = shift;
+ my @trees;
+ # Parse the result into a tree
+ my $forest = Bio::Phylo::IO->parse(
+ -format => 'newick',
+ -string => $newick,
+ );
+ # Turn the tree into a graph, starting with the root node
+ foreach my $tree ( @{$forest->get_entities} ) {
+ push( @trees, _graph_from_bio( $tree ) );
+ }
+ return \@trees;
+}
+
+=head2 newick_to_svg( $newick_string )
+
+Uses the FigTree utility (if installed) to transform the given Newick tree(s)
+into a graph visualization.
+
+=cut
+
+sub newick_to_svg {
+ my $newick = shift;
+ my $program = File::Which::which( 'figtree' );
+ unless( -x $program ) {
+ throw( "FigTree commandline utility not found in path" );
+ }
+ my $svg;
+ my $nfile = File::Temp->new();
+ print $nfile $newick;
+ close $nfile;
+ my @cmd = ( $program, '-graphic', 'SVG', $nfile );
+ run( \@cmd, ">", binary(), \$svg );
+ return decode_utf8( $svg );
+}
+
+sub _graph_from_bio {
+ my $tree = shift;
+ my $graph = Graph->new( 'undirected' => 1 );
+ # Give all the intermediate anonymous nodes a name.
+ my $i = 0;
+ foreach my $n ( @{$tree->get_entities} ) {
+ next if $n->get_name;
+ $n->set_name( $i++ );
+ }
+ my $root = $tree->get_root->get_name;
+ $graph->add_vertex( $root );
+ _add_tree_children( $graph, $root, $tree->get_root->get_children() );
+ return $graph;
+}
+
+sub _add_tree_children {
+ my( $graph, $parent, $tree_children ) = @_;
+ foreach my $c ( @$tree_children ) {
+ my $child = $c->get_name;
+ $graph->add_vertex( $child );
+ $graph->add_path( $parent, $child );
+ _add_tree_children( $graph, $child, $c->get_children() );
+ }
+}
+
+sub throw {
+ Text::Tradition::Error->throw(
+ 'ident' => 'StemmaUtil error',
+ 'message' => $_[0],
+ );
+}
+
+1;
+
+=head1 LICENSE
+
+This package is free software and is provided "as is" without express
+or implied warranty. You can redistribute it and/or modify it under
+the same terms as Perl itself.
+
+=head1 AUTHOR
+
+Tara L Andrews E<lt>aurum@cpan.orgE<gt>
projects / scpubgit/stemmatology.git / blobdiff