added tests/code to set type in features/subfeatures in parsed Genban…

…k JSON
Arabidopsis-Information-Portal · Jul 16, 2013 · 5be9582 · 5be9582
1 parent 7e0dc62
commit 5be9582
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Showing 2 changed files with 13 additions and 7 deletions.
diff --git a/src/perl5/Bio/JBrowse/FeatureStream/Genbank.pm b/src/perl5/Bio/JBrowse/FeatureStream/Genbank.pm
@@ -46,6 +46,7 @@ sub _aggregate_features_from_gbk_record {
     my $startStop = _extractStartStopFromJoinToken( $f->{FEATURES}->[$indexTopLevel] );
     $f->{'start'} = $startStop->[0] + $offset + 1;
     $f->{'end'} = $startStop->[1] + $offset;
+    $f->{'type'} = $f->{FEATURES}->[$indexTopLevel]->{'name'};
 
     # add subfeatures
     $f->{'subfeatures'} = ();
@@ -55,10 +56,13 @@ sub _aggregate_features_from_gbk_record {
 	$startStop->[0] += $offset;
 	$startStop->[1] += $offset;
 	$startStop->[0]++;
-	my $newFeature = {'start' => $startStop->[0] || 0,
-			  'end' => $startStop->[1] || 0,
-			  'foo' => 'null','foo1' => 'null','foo2' => 'null','foo3' => 'null','foo4' => 'null','foo5' => 'null','foo6' => 'null','foo7' => 'null','foo8' => 'null','foo9' => 'null','foo10' => 'null','foo11' => 'null','foo12' => 'null','foo13' => 'null','foo14' => 'null',
-			 };
+ 	my $newFeature = {'start' => $startStop->[0] || 0,
+ 			  'end' => $startStop->[1] || 0,
+ 			  'type' => $f->{FEATURES}->[$i]->{'name'} || 'null',
+ 			  'foo1' => 'null','foo2' => 'null','foo3' => 'null','foo4' => 'null','foo5' => 'null','foo6' => 'null','foo7' => 'null',
+ 			  'foo8' => 'null','foo9' => 'null','foo10' => 'null','foo11' => 'null','foo12' => 'null','foo13' => 'null','foo14' => 'null',
+ 			  'foo14' => 'null'
+ 			 };
 	push @{$f->{'subfeatures'}}, $newFeature;
       }
     }

diff --git a/tests/perl_tests/flatfile-to-json.pl.t b/tests/perl_tests/flatfile-to-json.pl.t
@@ -348,10 +348,11 @@ for my $testfile ( "tests/data/au9_scaffold_subset.gff3", "tests/data/au9_scaffo
     # test start/stop of parent feature (full record)
     ok( $trackdata->{'trackData.json'}->{'intervals'}->{'nclist'}->[0]->[1] == 5001, "got right start coordinate (full record)" );
     ok( $trackdata->{'trackData.json'}->{'intervals'}->{'nclist'}->[0]->[2] == 10950, "got right stop coordinate (full record)" );
+    ok( $trackdata->{'trackData.json'}->{'intervals'}->{'nclist'}->[0]->[17] eq 'mRNA', "got right type in parent feature (full record)" );
 
     # test that the right attributes are present
      is_deeply( [sort(@{$trackdata->{'trackData.json'}->{'intervals'}->{'classes'}->[0]->{'attributes'}})], 
-		[sort(@{[ 'Start', 'End',  'Strand',  'COMMENT',  'DEFINITION',  'CLASSIFICATION',  'LOCUS', 'FEATURES',  'KEYWORDS',  'SEQUENCE',  'ACCESSION',  'Seq_id',  'NCBI_TAXON_ID', 'MOL_TYPE',  'ORIGIN',  'ORGANISM',  'VERSION',  'SOURCE',  'Subfeatures']})],
+		[sort(@{[ 'Start', 'End',  'Strand',  'COMMENT',  'DEFINITION',  'CLASSIFICATION',  'LOCUS', 'FEATURES',  'KEYWORDS',  'SEQUENCE',  'ACCESSION',  'Seq_id',  'NCBI_TAXON_ID', 'MOL_TYPE',  'ORIGIN',  'ORGANISM',  'Type', 'VERSION',  'SOURCE',  'Subfeatures']})],
 		'got the right attributes in trackData.json')
 	 or diag $trackdata->{'trackData.json'}->{'intervals'}->{'classes'}->[0]->{'attributes'};
 
@@ -369,12 +370,13 @@ for my $testfile ( "tests/data/au9_scaffold_subset.gff3", "tests/data/au9_scaffo
 
     my $subfeatures = $trackdata->{'trackData.json'}->{'intervals'}->{'nclist'}->[0]->[$actualSubFeatureIndex];
     ok ( scalar @{$subfeatures} == 15, "got the right number of subfeatures");
-    ok ( scalar(@{$subfeatures->[0]}) == scalar(@{$trackdata->{'trackData.json'}->{'intervals'}->{'classes'}->[0]->{'attributes'}}),
-	 "subfeature array is same length as attribute array");
+    ok ( scalar(@{$subfeatures->[0]}) + 1 == scalar(@{$trackdata->{'trackData.json'}->{'intervals'}->{'classes'}->[0]->{'attributes'}}),
+	 "subfeature array is the right length (length of attribute array + 1)");
     # test first subfeature completely
     ok ( exists $subfeatures->[0]->[0] && $subfeatures->[0]->[0] == 1, "first item set correctly in subfeature");
     ok ( exists $subfeatures->[0]->[1] && $subfeatures->[0]->[1] == 5001, "start set correctly in subfeature") || diag $subfeatures->[0]->[1];
     ok ( exists $subfeatures->[0]->[2] && $subfeatures->[0]->[2] == 5114, "end set correctly in subfeature") || diag $subfeatures->[0]->[2];
+    ok ( exists $subfeatures->[0]->[2] && $subfeatures->[0]->[17] eq 'exon', "type set correctly in subfeature") || diag $subfeatures->[0]->[2];
     undef;
 
 }