Option to ignore leaves with missing trait value when doing add_trait()

bioperl · May 21, 2012 · 8131205 · 8131205
1 parent f290574
commit 8131205
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Showing 3 changed files with 39 additions and 33 deletions.
diff --git a/Bio/Tree/TreeFunctionsI.pm b/Bio/Tree/TreeFunctionsI.pm
@@ -1133,12 +1133,14 @@ sub move_id_to_bootstrap{
            are added to leaf nodes as a tag named $key using the add_tag_value()
            method. This means that you can retrieve the trait values using the
            get_tag_values() method (see the documentation for Bio::Tree::Node).
-           If a leaf node has no value in the trait file, an exception is thrown.
  Returns : Trait name (a scalar) on success, undef on failure (for example, if
            the column index requested was too large).
- Args    : Name of trait file (scalar string)
-           Index of trait file column (scalar int). Note that numbering starts
-           at 0. Default: 1 (second column)
+ Args    : * Name of trait file (scalar string).
+           * Index of trait file column (scalar int). Note that numbering starts
+             at 0. Default: 1 (second column).
+           * Ignore missing values. Typically, if a leaf node has no value in
+             the trait file, an exception is thrown. If you set this option to
+             1, then no trait will be given to the node (no exception thrown).
 
 =cut
 
@@ -1148,43 +1150,44 @@ sub _read_trait_file {
     my $column = shift || 1;
 
     my $trait_name;
-    my $traits;
+    my $trait_values;
     open my $TRAIT, "<", $file or $self->("Could not open file $file: $!\n");
 
     my $first_line = 1;
     while (<$TRAIT>) {
+        chomp;
         s/['"]//g;
-        my @line = split;
+        my @line = split /\t/;
         if ($first_line) {
             $first_line = 0;
             $trait_name = $line[$column];
             next;
         }
         last unless $line[0];
-        $traits->{$line[0]} = $line[$column];
+        $trait_values->{$line[0]} = $line[$column];
     }
 
     close $TRAIT;
-    return $trait_name, $traits;
+    return $trait_name, $trait_values;
 }
 
 sub add_trait {
-    my $self = shift;
-    my $file = shift;
-    my $column = shift;
+    my ($self, $file, $column, $ignore) = @_;
+    $ignore = 0 if not defined $ignore;
 
-    my ($trait_name, $traits) = $self->_read_trait_file($file, $column);
+    my ($trait_name, $trait_values) = $self->_read_trait_file($file, $column);
 
     if (defined $trait_name) {
         for my $node ($self->get_leaf_nodes) {
             # strip quotes from the node id
             $node->id($1) if $node->id =~ /^['"]+(.*)['"]+$/;
             eval {
                 $node->verbose(2);
-                $node->add_tag_value($trait_name, $traits->{ $node->id } );
+                $node->add_tag_value($trait_name, $trait_values->{ $node->id } );
             };
-            $self->throw("No trait for node [".$node->id."/".$node->internal_id."]")
-               if $@;
+            if ($@ && (not $ignore)) {
+                $self->throw("No trait for node [".$node->id."/".$node->internal_id."]")
+            }
         }
     }
     return $trait_name;

diff --git a/t/Tree/TreeStatistics.t b/t/Tree/TreeStatistics.t
@@ -7,7 +7,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin(-tests => 41);
+    test_begin(-tests => 42);
 
     use_ok('Bio::TreeIO');
     use_ok('Bio::Tree::Statistics');
@@ -29,6 +29,9 @@ is $stats->cherries($tree, $node), 4, 'cherries';
 my $key = $tree->add_trait(test_input_file('traits.tab'), 4);
 is $key, undef, 'read traits'; # exceeded column number
 
+$key = $tree->add_trait(test_input_file('traits.tab'), 2, 1);
+is $key, 'disp'; # one leaf has a missing trait value, but ignore it
+
 $key = $tree->add_trait(test_input_file('traits.tab'), 3);
 is $key, 'intermediate';
 

diff --git a/t/data/traits.tab b/t/data/traits.tab
@@ -1,17 +1,17 @@
-"id"	"assoc"	"disp"	"intermediate"
-1	"blue"	"blue"	"red"
-2	"blue"	"red"	"blue"
-3	"blue"	"blue"	"blue"
-4	"blue"	"red"	"blue"
-5	"blue"	"blue"	"red"
-6	"blue"	"red"	"blue"
-7	"blue"	"blue"	"blue"
-8	"blue"	"red"	"blue"
-9	"red"	"blue"	"red"
-10	"red"	"red"	"red"
-11	"red"	"blue"	"blue"
-12	"red"	"red"	"blue"
-13	"red"	"blue"	"red"
-14	"red"	"red"	"red"
-15	"red"	"blue"	"red"
-16	"red"	"red"	"red"
+"id"	"assoc"	disp	"intermediate"
+1	"blue"	blue	"red"
+2	"blue"		"blue"
+3	"blue"	blue	"blue"
+4	"blue"	red	"blue"
+5	"blue"	blue	"red"
+6	"blue"	red	"blue"
+7	"blue"	blue	"blue"
+8	"blue"	red	"blue"
+9	"red"	blue	"red"
+10	"red"	red	"red"
+11	"red"	blue	"blue"
+12	"red"	red	"blue"
+13	"red"	blue	"red"
+14	"red"	red	"red"
+15	"red"	blue	"red"
+16	"red"	red	"red"