# For each column in the table, group the readings by witness.
-my $useful_vars = 0;
+my $used_vars = 0;
foreach my $i ( 0 .. $#$all_wits_table ) {
my $rdg_wits = {};
my $col_rdgs = shift @$all_wits_table;
my( $groups, $readings ) = useful_variant( $rdg_wits );
next unless $groups && $readings;
- # For all the groups with more than one member, make a group that contains
- # all contiguous vertices to connect them.
- # TODO Need to do pairwise comparison of groups - a variant location can
- # have both coincidental and genealogical variants!
+ # We can look up witnesses for a reading; we also want to look up readings
+ # for a given witness.
+ my $group_readings = {};
+ foreach my $x ( 0 .. $#$groups ) {
+ $group_readings->{wit_stringify( $groups->[$x] )} = $readings->[$x];
+ }
+
+ # For all the groups with more than one member, collect the list of all
+ # contiguous vertices needed to connect them.
+ # TODO: deal with a.c. reading logic
+ my $conflict = analyze_variant_location( $group_readings, $groups, $stemma->apsp );
+ print wit_stringify( $groups ) . ' - ' . join( " / ", @$readings ) . "\n";
+ foreach my $rdg ( keys %$conflict ) {
+ my $var = $conflict->{$rdg};
+ print "\tReadings '$rdg' and '$var' are not genealogical\n";
+ }
+
+ # Now run the same analysis given a distance tree.
+ my $distance_apsp = $stemma->distance_trees->[0]->APSP_Floyd_Warshall();
+ $conflict = analyze_variant_location( $group_readings, $groups, $distance_apsp );
+ foreach my $rdg ( keys %$conflict ) {
+ my $var = $conflict->{$rdg};
+ print "\tReadings '$rdg' and '$var' disregarded by parsimony\n";
+ }
+
+ # Record that we used this variant in an analysis
+ $used_vars++;
+
+}
+print "Found $used_vars useful variants in this analysis\n";
+
+sub analyze_variant_location {
+ my( $group_readings, $groups, $apsp ) = @_;
my %contig;
- my $conflict;
- foreach my $g ( @$groups ) {
- my @members = split( /,/, $g );
+ my $conflict = {};
+ foreach my $g ( sort { scalar @$b <=> scalar @$a } @$groups ) {
+ my @members = @$g;
+ my $gst = wit_stringify( $g );
+ map { $contig{$_} = $gst } @members; # The witnesses need themselves to be
+ # in their collection.
next unless @members > 1;
- map { $contig{$_} = $g } @members;
my $curr = pop @members;
foreach my $m ( @members ) {
- foreach my $v ( $stemma->apsp->path_vertices( $curr, $m ) ) {
- $contig{$v} = $g unless exists $contig{$v};
- next if $contig{$v} eq $g;
- # print STDERR "Conflict at $v between group $g and group "
+ foreach my $v ( $apsp->path_vertices( $curr, $m ) ) {
+ $contig{$v} = $gst unless exists $contig{$v};
+ next if $contig{$v} eq $gst;
+ # print STDERR "Conflict at $v between group $gst and group "
# . $contig{$v} . "\n";
- $conflict = 1;
+ # Record what is conflicting.
+ $conflict->{$group_readings->{$gst}} = $group_readings->{$contig{$v}};
}
}
}
- print join( " / ", @$groups ) . ' - ' . join( " / ", @$readings ) . ' - ';
- print $conflict ? "coincidental" : "genealogical";
- print "\n";
- $useful_vars++;
-
+ return $conflict;
}
-print "Found $useful_vars useful variants\n";
# Add the variant, subject to a.c. representation logic.
# This assumes that we will see the 'main' version before the a.c. version.
return( undef, undef ) if $total <= 1;
my( $groups, $text );
foreach my $var ( keys %$readings ) {
- push( @$groups, join( ',', @{$readings->{$var}} ) );
+ push( @$groups, $readings->{$var} );
push( @$text, $var );
}
return( $groups, $text );
}
+
+# Take an array of witness groupings and produce a string like
+# A,B / C,D,E / F
+
+sub wit_stringify {
+ my $groups = shift;
+ my @gst;
+ # If we were passed an array of witnesses instead of an array of
+ # groupings, then "group" the witnesses first.
+ unless( ref( $groups->[0] ) ) {
+ my $mkgrp = [ $groups ];
+ $groups = $mkgrp;
+ }
+ foreach my $g ( @$groups ) {
+ push( @gst, join( ',', @$g ) );
+ }
+ return join( ' / ', @gst );
+}
+
\ No newline at end of file
package Text::Tradition::Stemma;
+use Bio::Phylo::IO;
use File::chdir;
use File::Temp;
-use IPC::Run qw/ run /;
-use Moose;
-use Text::Tradition::Collation::Position;
use Graph;
use Graph::Reader::Dot;
+use IPC::Run qw/ run /;
+use Moose;
+use Text::Balanced qw/ extract_bracketed /;
has collation => (
is => 'ro',
is => 'rw',
isa => 'Graph',
);
+
+has distance_trees => (
+ is => 'ro',
+ isa => 'ArrayRef[Graph]',
+ writer => '_save_distance_trees',
+ predicate => 'has_distance_trees',
+ );
sub BUILD {
my( $self, $args ) = @_;
$self->apsp( $undirected->APSP_Floyd_Warshall() );
}
}
-
+
+before 'distance_trees' => sub {
+ my $self = shift;
+ my %args = @_;
+ # TODO allow specification of method for calculating distance tree
+ if( $args{'recalc'} || !$self->has_distance_trees ) {
+ # We need to make a tree before we can return it.
+ my( $ok, $result ) = $self->run_phylip_pars();
+ if( $ok ) {
+ $self->_save_distance_trees( _parse_newick( $result ) );
+ } else {
+ warn "Failed to calculate distance tree: $result";
+ }
+ }
+};
sub make_character_matrix {
my $self = shift;
}
}
if( scalar( keys %unique ) > 8 ) {
- warn "Have more than 8 variants on this location; pars will break";
+ warn "Have more than 8 variants on this location; phylip will break";
}
my @chars = map { $_ ? $unique{$_} : $unique{'__UNDEF__' } } @$row;
return @chars;
}
-sub pars_input {
+sub phylip_pars_input {
my $self = shift;
$self->make_character_matrix unless $self->has_character_matrix;
my $matrix = '';
return $matrix;
}
-sub run_pars {
+sub run_phylip_pars {
my $self = shift;
# Set up a temporary directory for all the default Phylip files.
my $phylip_dir = File::Temp->newdir();
- print STDERR $phylip_dir . "\n";
# $phylip_dir->unlink_on_destroy(0);
# We need an infile, and we need a command input file.
open( MATRIX, ">$phylip_dir/infile" ) or die "Could not write $phylip_dir/infile";
- print MATRIX $self->pars_input();
+ print MATRIX $self->phylip_pars_input();
close MATRIX;
open( CMD, ">$phylip_dir/cmdfile" ) or die "Could not write $phylip_dir/cmdfile";
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;
+}
+
+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() );
+ }
+}
+
no Moose;
__PACKAGE__->meta->make_immutable;
projects / scpubgit/stemmatology.git / commitdiff