Force ID field for all gb files converted to gff3

bioperl · Jul 30, 2010 · c1abbd1 · c1abbd1 · rbuels · Aug 2, 2010
1 parent b0b52cc
commit c1abbd1
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diff --git a/Bio/Tools/GFF.pm b/Bio/Tools/GFF.pm
@@ -1033,6 +1033,13 @@ sub _gff3_string {
 	unshift @all_tags, $t if $feat->has_tag($t);
     }
 
+    #force a Name tag for anything that has an ID
+    my %all_tags;
+    map $all_tags{$_} = 1, @all_tags;
+    if ($all_tags{'ID'} && ! $all_tags{'Name'}) {
+	push @groups, "Name=".join(",",$feat->each_tag_value('ID'));
+    }
+
     for my $tag ( @all_tags ) {
     next if exists $SKIPPED_TAGS{$tag};
 	# next if $tag eq 'Target';

diff --git a/Build.PL b/Build.PL
@@ -64,6 +64,7 @@ my $build = Bio::Root::Build->new(
                             'perl'                      => '5.6.1',
                             'IO::String'                => 0,
                             'DB_File'                   => 0,
+			    'YAML'                      => 0,
                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
                             'ExtUtils::Manifest'        => '1.52', # allows spaces in file names