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::StemmaUtil qw/ phylip_pars_input /;
+use Text::Tradition::Error;
+use Text::Tradition::StemmaUtil qw/ character_input phylip_pars parse_newick /;
use Moose;
has collation => (
sub graph_from_dot {
my( $self, $dotfh ) = @_;
- # Assume utf-8
- binmode( $dotfh, ':utf8' );
my $reader = Graph::Reader::Dot->new();
my $graph = $reader->read_graph( $dotfh );
if( $graph ) {
unless $self->graph->has_vertex_attribute( $v, 'class' );
}
} else {
- warn "Failed to parse dot in $dotfh";
+ throw( "Failed to parse dot in $dotfh" );
}
}
my( $self, $opts ) = @_;
# Get default and specified options
- my %graphopts = ();
+ my %graphopts = (
+ # 'ratio' => 1,
+ );
my %nodeopts = (
'fontsize' => 11,
- 'hshape' => 'plaintext', # Shape for the hypothetical nodes
- 'htext' => '*',
'style' => 'filled',
'fillcolor' => 'white',
+ 'color' => 'white',
'shape' => 'ellipse', # Shape for the extant nodes
);
my %edgeopts = (
- 'arrowhead' => 'open',
+ 'arrowhead' => 'none',
);
@graphopts{ keys %{$opts->{'graph'}} } = values %{$opts->{'graph'}}
if $opts->{'graph'};
## Print out the global attributes
push( @dotlines, _make_dotline( 'graph', %graphopts ) ) if keys %graphopts;
push( @dotlines, _make_dotline( 'edge', %edgeopts ) ) if keys %edgeopts;
- ## Delete our special attributes from the node set before continuing
- my $hshape = delete $nodeopts{'hshape'};
- my $htext = delete $nodeopts{'htext'};
push( @dotlines, _make_dotline( 'node', %nodeopts ) ) if keys %nodeopts;
# Add each of the nodes.
foreach my $n ( $self->graph->vertices ) {
- if( $self->graph->get_vertex_attribute( $n, 'class' ) eq 'hypothetical' ) {
- # Apply our display settings for hypothetical nodes.
- push( @dotlines, _make_dotline( $n, 'shape' => $hshape, 'label' => $htext ) );
+ if( $self->graph->has_vertex_attribute( $n, 'label' ) ) {
+ my $ltext = $self->graph->get_vertex_attribute( $n, 'label' );
+ push( @dotlines, _make_dotline( $n, 'label' => $ltext ) );
} else {
# Use the default display settings.
push( @dotlines, " $n;" );
my( $ok, $result ) = $self->$dsub();
if( $ok ) {
# Save the resulting trees
- my $trees = _parse_newick( $result );
+ my $trees = parse_newick( $result );
$self->_save_distance_trees( $trees );
$self->distance_program( $args{'program'} );
} else {
- warn "Failed to calculate distance trees: $result";
+ throw( "Failed to calculate distance trees: $result" );
}
}
};
sub run_phylip_pars {
- my $self = shift;
-
- # 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 phylip_pars_input( $self->collation->make_alignment_table() );
- close MATRIX;
-
- open( CMD, ">$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 ) {
- return( undef, "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, "$phylip_dir/outtree" ) or die "Could not open outtree for read";
- @outtree = <TREE>;
- close TREE;
- }
- return( 1, join( '', @outtree ) ) if @outtree;
-
- my @error;
- if( -f "$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!" );
- }
- return( undef, join( '', @error ) );
-}
-
-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;
+ my $self = shift;
+ my $cdata = character_input( $self->collation->make_alignment_table() );
+ return phylip_pars( $cdata );
}
-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 throw {
+ Text::Tradition::Error->throw(
+ 'ident' => 'Stemma error',
+ 'message' => $_[0],
+ );
}
-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() );
- }
-}
no Moose;
__PACKAGE__->meta->make_immutable;
projects / scpubgit/stemmatology.git / blobdiff