add --noSubfeature option to flatfile-to-json.pl

Arabidopsis-Information-Portal · Jul 24, 2013 · 5a71902 · 5a71902
1 parent bbb82b6
commit 5a71902
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Showing 4 changed files with 22 additions and 30 deletions.
diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl
@@ -22,12 +22,9 @@ =head1 USAGE
       [ --out <output directory> ]                                            \
       [ --key <human-readable track name> ]                                   \
       [ --className <CSS class name for displaying features> ]                \
-      [ --getType ]                                                           \
-      [ --getPhase ]                                                          \
-      [ --getSubfeatures ]                                                    \
-      [ --getLabel ]                                                          \
       [ --urltemplate "http://example.com/idlookup?id={id}" ]                 \
       [ --arrowheadClass <CSS class> ]                                        \
+      [ --noSubfeatures ]                                                     \
       [ --subfeatureClasses '{ JSON-format subfeature class map }' ]          \
       [ --clientConfig '{ JSON-format extra configuration for this track }' ] \
       [ --thinType <BAM -thin_type> ]                                         \
@@ -77,26 +74,14 @@ =head2 Optional
 
 CSS class for features.  Defaults to "feature".
 
-=item --getType
-
-Include the type of the features in the JSON.
-
-=item --getPhase
-
-Include the phase of the features in the JSON.
-
-=item --getSubfeatures
-
-Include subfeatures in the JSON.
-
-=item --getLabel
-
-Include a label for the features in the JSON.
-
 =item --urltemplate "http://example.com/idlookup?id={id}"
 
 Template for a URL to be visited when features are clicked on.
 
+=item --noSubfeatures
+
+Do not format subfeature data.
+
 =item --arrowheadClass <CSS class>
 
 CSS class for arrowheads.

diff --git a/release-notes.txt b/release-notes.txt
@@ -33,6 +33,10 @@
    run like:
        bin/prepare-refseqs.pl --sizes myrefs.sizes
 
+ * Added a '--noSubfeatures' option for flatfile-to-json.pl to skip
+   importing subfeatures (since `--getSubfeatures` is on by default
+   for some time).
+
  * The "JBrowse" link on the left side of the menu bar, and the
    browser title, now display the "About this browser" title instead
    of JBrowse, if `aboutThisBrowser` is set in the configuration.

diff --git a/src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm b/src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
@@ -40,6 +40,7 @@ sub option_definitions {
         "getType",
         "getPhase",
         "getSubs|getSubfeatures",
+        "noSubfeatures",
         "getLabel",
         "urltemplate=s",
         "menuTemplate=s",
@@ -83,9 +84,6 @@ sub run {
 
 
     my %config = (
-        type         => $self->opt('getType') || $self->opt('type') ? 1 : 0,
-        phase        => $self->opt('getPhase'),
-        subfeatures  => $self->opt('getSubs'),
         style          => {
             %{ $self->opt('clientConfig') || {} },
             className      => $self->opt('cssClass'),
@@ -127,6 +125,7 @@ sub make_gff_stream {
 
     return Bio::JBrowse::FeatureStream::GFF3_LowLevel->new(
         parser => $p,
+        no_subfeatures => $self->opt('noSubfeatures'),
         track_label => $self->opt('trackLabel')
      );
 }
@@ -145,6 +144,7 @@ sub make_bed_stream {
         );
 
     return Bio::JBrowse::FeatureStream::BioPerl->new(
+        no_subfeatures => $self->opt('noSubfeatures'),
         stream => sub { $io->next_feature },
         track_label => $self->opt('trackLabel'),
     );

diff --git a/src/perl5/Bio/JBrowse/FeatureStream.pm b/src/perl5/Bio/JBrowse/FeatureStream.pm
@@ -30,15 +30,18 @@ sub flatten_to_feature {
               @{$f}{ @{$class->{fields}} }
             );
 
-    for my $subfeature_field (qw( subfeatures derived_features )) {
-        if( my $sfi = $class->{field_idx}{ $subfeature_field } ) {
-            $f[ $sfi+1 ] = [
-                map {
-                    $self->flatten_to_feature($_)
-                } @{$f[$sfi+1]}
-            ];
+    unless( $self->{no_subfeatures} ) {
+        for my $subfeature_field (qw( subfeatures derived_features )) {
+            if ( my $sfi = $class->{field_idx}{ $subfeature_field } ) {
+                $f[ $sfi+1 ] = [
+                    map {
+                        $self->flatten_to_feature($_)
+                    } @{$f[$sfi+1]}
+                    ];
+            }
         }
     }
+
     # use Data::Dump 'dump';
     # print dump($_)."\n" for \@f, $class;