use File::Temp;
use JSON;
use Text::Tradition::Collation;
-use Text::Tradition::StemmaUtil qw/ phylip_pars_input /;
+use Text::Tradition::StemmaUtil qw/ character_input /;
BEGIN { extends 'Catalyst::Controller' }
my $json = $c->request->params->{'alignment'};
$c->log->debug( $json );
my $table = from_json( $json );
- my $matrix = phylip_pars_input( $table );
+ my $matrix = character_input( $table );
$c->stash->{'result'} = { 'matrix' => $matrix };
$c->forward( 'View::JSON' );
}
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::StemmaUtil qw/ character_input phylip_pars parse_newick /;
use Moose;
has collation => (
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 {
};
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;
-}
-
-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() );
- }
+ my $self = shift;
+ my $cdata = character_input( $self->collation->make_alignment_table() );
+ return phylip_pars( $cdata );
}
no Moose;
use warnings;
use Exporter 'import';
use vars qw/ @EXPORT_OK /;
-@EXPORT_OK = qw/ phylip_pars_input /;
+use Bio::Phylo::IO;
+use File::chdir;
+use File::Temp;
+use File::Which;
+use Graph;
+use Graph::Reader::Dot;
+use IPC::Run qw/ run binary /;
+@EXPORT_OK = qw/ make_character_matrix character_input phylip_pars parse_newick /;
sub make_character_matrix {
my( $table ) = @_;
return @chars;
}
-sub phylip_pars_input {
+sub character_input {
my $table = shift;
my $character_matrix = make_character_matrix( $table );
my $input = '';
return $input;
}
+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 ) {
+ 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;
+}
+
+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() );
+ }
+}
use Test::More;
use lib 'lib';
use Text::Tradition;
-use Text::Tradition::StemmaUtil qw/ phylip_pars_input /;
+use Text::Tradition::StemmaUtil qw/ make_character_matrix /;
use XML::LibXML;
use XML::LibXML::XPathContext;
is( $stemma->graph, '1-2,1-A,2-B,2-C', "Got the correct graph" );
# Test for character matrix creation
-my $m = phylip_pars_input( $c->make_alignment_table() );
+my $m = make_character_matrix( $c->make_alignment_table() );
## check number of rows
-my $expected = "\t3\t18\n";
-$expected .= 'A AAAAAAAXAAAAAAAAAA
-B AXXXAAAAAABABAABAA
-C AXXXAAAAABAAAAAXBB';
-$expected .= "\n";
-is( $m, $expected, "Got the right pars input" );
-# is( scalar @$m, 3, "Found three witnesses in char matrix" );
-# ## check number of columns
-# is( scalar( @{$m->[0]} ), 19, "Found 18 rows plus sigla in char matrix" );
-# ## check matrix
-# my %expected = (
-# 'A' => 'AAAAAAAXAAAAAAAAAA',
-# 'B' => 'AXXXAAAAAABABAABAA',
-# 'C' => 'AXXXAAAAABAAAAAXBB',
-# );
-# my @wits = map { shift @$_; } @$m;
-# map { s/\s+//g } @wits;
-# foreach my $i ( 0 .. $#wits ) {
-# my $w = $wits[$i];
-# is( join( '', @{$m->[$i]} ), $expected{$w}, "Row for witness $w is correct" );
-# }
+is( scalar @$m, 3, "Found three witnesses in char matrix" );
+ ## check number of columns
+is( scalar( @{$m->[0]} ), 19, "Found 18 rows plus sigla in char matrix" );
+ ## check matrix
+my %expected = (
+ 'A' => 'AAAAAAAXAAAAAAAAAA',
+ 'B' => 'AXXXAAAAAABABAABAA',
+ 'C' => 'AXXXAAAAABAAAAAXBB',
+ );
+my @wits = map { shift @$_; } @$m;
+map { s/\s+//g } @wits;
+foreach my $i ( 0 .. $#wits ) {
+ my $w = $wits[$i];
+ is( join( '', @{$m->[$i]} ), $expected{$w}, "Row for witness $w is correct" );
+}
# Test that pars runs
SKIP: {
projects / scpubgit/stemmatology.git / commitdiff