include Score in feature data made by flatfile-to-json.pl by default,…

… references #72
GMOD · Apr 17, 2012 · a348996 · a348996
1 parent 43ef2b0
commit a348996
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Showing 2 changed files with 12 additions and 12 deletions.
diff --git a/lib/Bio/JBrowse/Cmd/FlatFileToJson/FeatureStream.pm b/lib/Bio/JBrowse/Cmd/FlatFileToJson/FeatureStream.pm
@@ -17,7 +17,7 @@ sub new {
 sub flatten_to_feature {
     my ( $self, $f, $class_index ) = @_;
     my @f = ( $class_index || 0,
-              @{$f}{qw{ start end strand source phase type }},
+              @{$f}{qw{ start end strand source phase type score }},
               (map $f->{attributes}{$_}[0], qw(ID Name)),
               [ map $self->flatten_to_feature($_,1), @{$f->{child_features}} ],
             );
@@ -45,7 +45,7 @@ sub flatten_to_name {
     return \@namerec;
 }
 
-sub featureHeaders    { [qw[ Start End Strand Source Phase Type Id Name Subfeatures ]] }
+sub featureHeaders    { [qw[ Start End Strand Source Phase Type Score Id Name Subfeatures ]] }
 *subfeatureHeaders = \&featureHeaders;
 sub startIndex        { 1 }
 sub endIndex          { 2 }

diff --git a/tests/perl_tests/flatfile-to-json.pl.t b/tests/perl_tests/flatfile-to-json.pl.t
@@ -88,9 +88,9 @@ sub tempdir {
         scalar( @{$cds_trackdata->{histograms}{stats}}),
         'have stats for each precalculated hist' );
 
-    is( ref $cds_trackdata->{intervals}{nclist}[2][9], 'ARRAY', 'exonerate mRNA has its subfeatures' )
+    is( ref $cds_trackdata->{intervals}{nclist}[2][10], 'ARRAY', 'exonerate mRNA has its subfeatures' )
        or diag explain $cds_trackdata;
-    is( scalar @{$cds_trackdata->{intervals}{nclist}[2][9]}, 5, 'exonerate mRNA has 5 subfeatures' );
+    is( scalar @{$cds_trackdata->{intervals}{nclist}[2][10]}, 5, 'exonerate mRNA has 5 subfeatures' );
 
     my $tracklist = $read_json->('trackList.json');
     is_deeply( $tracklist->{tracks}[1]{style},
@@ -127,9 +127,9 @@ sub tempdir {
     my $read_json = sub { slurp( $tempdir, @_ ) };
     my $cds_trackdata = $read_json->(qw( tracks AU_mRNA Group1.33 trackData.json ));
     is( $cds_trackdata->{featureCount}, 1, 'got right feature count' ) or diag explain $cds_trackdata;
-    is( ref $cds_trackdata->{intervals}{nclist}[0][9], 'ARRAY', 'mRNA has its subfeatures' )
+    is( ref $cds_trackdata->{intervals}{nclist}[0][10], 'ARRAY', 'mRNA has its subfeatures' )
        or diag explain $cds_trackdata;
-    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][9]}, 7, 'mRNA has 7 subfeatures' );
+    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][10]}, 7, 'mRNA has 7 subfeatures' );
 
     my $tracklist = $read_json->( 'trackList.json' );
     is( $tracklist->{tracks}[0]{key}, 'AU mRNA', 'got a tracklist' ) or diag explain $tracklist;
@@ -155,9 +155,9 @@ sub tempdir {
     # check that we got the same data as before
     $cds_trackdata = $read_json->(qw( tracks AU_mRNA Group1.33 trackData.json ));
     is( $cds_trackdata->{featureCount}, 1, 'got right feature count' ) or diag explain $cds_trackdata;
-    is( ref $cds_trackdata->{intervals}{nclist}[0][9], 'ARRAY', 'mRNA has its subfeatures' )
+    is( ref $cds_trackdata->{intervals}{nclist}[0][10], 'ARRAY', 'mRNA has its subfeatures' )
        or diag explain $cds_trackdata;
-    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][9]}, 7, 'mRNA has 7 subfeatures' );
+    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][10]}, 7, 'mRNA has 7 subfeatures' );
 }
 
 {   #diag "running on single_au9_gene.gff3, testing that we emit 2 levels of subfeatures";
@@ -182,12 +182,12 @@ sub tempdir {
     my $read_json = sub { slurp( $tempdir, @_ ) };
     my $cds_trackdata = $read_json->(qw( tracks AU_mRNA Group1.33 trackData.json ));
     is( $cds_trackdata->{featureCount}, 1, 'got right feature count' ) or diag explain $cds_trackdata;
-    is( ref $cds_trackdata->{intervals}{nclist}[0][9], 'ARRAY', 'gene has its subfeatures' )
+    is( ref $cds_trackdata->{intervals}{nclist}[0][10], 'ARRAY', 'gene has its subfeatures' )
        or diag explain $cds_trackdata;
-    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][9]}, 1, 'gene has 1 subfeature' );
-    is( ref $cds_trackdata->{intervals}{nclist}[0][9][0][9], 'ARRAY', 'mRNA has its subfeatures' )
+    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][10]}, 1, 'gene has 1 subfeature' );
+    is( ref $cds_trackdata->{intervals}{nclist}[0][10][0][10], 'ARRAY', 'mRNA has its subfeatures' )
        or diag explain $cds_trackdata;
-    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][9][0][9]}, 7, 'mRNA has 7 subfeatures' );
+    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][10][0][10]}, 7, 'mRNA has 7 subfeatures' );
 }
 
 for my $testfile ( "tests/data/au9_scaffold_subset.gff3", "tests/data/au9_scaffold_subset_sync.gff3" ) {