add better tests for --type filtering argument to flatfile-to-json.pl

GMOD · Mar 7, 2012 · 6200533 · 6200533
1 parent ac9613d
commit 6200533
Showing 1 changed file with 102 additions and 66 deletions.
diff --git a/tests/perl_tests/flatfile-to-json.pl.t b/tests/perl_tests/flatfile-to-json.pl.t
@@ -4,75 +4,111 @@ use warnings;
 use Test::More;
 
 use File::Spec::Functions 'catfile';
-use File::Temp;
+use File::Temp ();
 use File::Copy::Recursive 'dircopy';
 
 use JsonGenerator;
 
-my $tempdir   = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
-diag "using temp dir $tempdir";
-my $read_json = sub { JsonGenerator::readJSON( catfile( $tempdir, @_ ) ) };
-dircopy( 'tests/data/volvox_formatted_refseqs', $tempdir );
-
-system $^X, 'bin/flatfile-to-json.pl', (
-    '--out' => $tempdir,
-    '--bed' => 'sample_data/raw/volvox/volvox-remark.bed',
-    '--trackLabel' => 'ExampleFeatures',
-    '--key' => 'Example Features',
-    '--autocomplete' => 'all',
-    '--cssClass' => 'feature2',
-    '--clientConfig' =>  '{"featureCss": "height: 8px;", "histScale": 2}',
-    );
-
-ok( ! $?, 'flatfile-to-json.pl ran ok on the volvox bed' );
-
-system $^X, 'bin/flatfile-to-json.pl', (
-    '--out' => $tempdir,
-    '--gff' => 'sample_data/raw/volvox/volvox.gff3',
-    '--trackLabel' => 'CDS',
-    '--key' => 'Predicted genes',
-    '--type' => 'CDS:predicted,mRNA:exonerate,mRNA:predicted',
-    '--autocomplete' => 'all',
-    '--cssClass' => 'cds',
-    '--getPhase',
-    '--getSubfeatures',
-    );
-
-ok( ! $?, 'flatfile-to-json.pl ran ok on the volvox gff3' );
-
-my $hist_output = $read_json->(qw( tracks ExampleFeatures ctgA hist-10000-0.json ));
-is_deeply( $hist_output, [4,3,4,3,4,1], 'got right histogram output' ) or diag explain( $hist_output );
-
-my $names_output = $read_json->(qw( tracks ExampleFeatures ctgA names.json ));
-is_deeply( $names_output->[3],
-           [
-             [
-               'f05'
-             ],
-             'ExampleFeatures',
-             'f05',
-             'ctgA',
-             4715,
-             5968,
-             undef
-           ],
-           'got the right names output'
-           ) or diag explain $names_output;
-
-my $cds_trackdata = $read_json->(qw( tracks CDS ctgA trackData.json ));
-is( $cds_trackdata->{featureCount}, 3, 'got right feature count' ) or diag explain $cds_trackdata;
-is( ref $cds_trackdata->{intervals}{nclist}[2][9], '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_deeply( $read_json->('trackList.json')->{tracks}[1]{config}{style},
-           { featureCss => 'height: 8px;',
-             histScale => 2,
-             className => 'feature2',
-           },
-           '--clientConfig option seems to work'
-         ) or diag explain $read_json->('trackList.json');
-
-#system "find $tempdir";
+sub run_with(@) {
+    system $^X, 'bin/flatfile-to-json.pl', @_;
+    ok( ! $?, 'flatfile-to-json.pl ran ok' );
+}
+
+sub tempdir {
+    my $tempdir   = File::Temp->newdir( CLEANUP => $ENV{KEEP_ALL} ? 0 : 1 );
+    #diag "using temp dir $tempdir";
+    return $tempdir;
+}
+
+{  #diag "running on volvox";
+
+    my $tempdir = tempdir();
+    my $read_json = sub { JsonGenerator::readJSON( catfile( $tempdir, @_ ) ) };
+    dircopy( 'tests/data/volvox_formatted_refseqs', $tempdir );
+
+    run_with (
+        '--out' => $tempdir,
+        '--bed' => 'sample_data/raw/volvox/volvox-remark.bed',
+        '--trackLabel' => 'ExampleFeatures',
+        '--key' => 'Example Features',
+        '--autocomplete' => 'all',
+        '--cssClass' => 'feature2',
+        '--clientConfig' =>  '{"featureCss": "height: 8px;", "histScale": 2}',
+        );
+
+    run_with (
+        '--out' => $tempdir,
+        '--gff' => 'sample_data/raw/volvox/volvox.gff3',
+        '--trackLabel' => 'CDS',
+        '--key' => 'Predicted genes',
+        '--type' => 'CDS:predicted,mRNA:exonerate,mRNA:predicted',
+        '--autocomplete' => 'all',
+        '--cssClass' => 'cds',
+        '--getPhase',
+        '--getSubfeatures',
+        );
+
+    my $hist_output = $read_json->(qw( tracks ExampleFeatures ctgA hist-10000-0.json ));
+    is_deeply( $hist_output, [4,3,4,3,4,1], 'got right histogram output' ) or diag explain( $hist_output );
+
+    my $names_output = $read_json->(qw( tracks ExampleFeatures ctgA names.json ));
+    is_deeply( $names_output->[3],
+               [
+                 [
+                   'f05'
+                 ],
+                 'ExampleFeatures',
+                 'f05',
+                 'ctgA',
+                 4715,
+                 5968,
+                 undef
+               ],
+               'got the right names output'
+               ) or diag explain $names_output;
+
+    my $cds_trackdata = $read_json->(qw( tracks CDS ctgA trackData.json ));
+    is( $cds_trackdata->{featureCount}, 3, 'got right feature count' ) or diag explain $cds_trackdata;
+    is( ref $cds_trackdata->{intervals}{nclist}[2][9], '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_deeply( $read_json->('trackList.json')->{tracks}[1]{config}{style},
+               { featureCss => 'height: 8px;',
+                 histScale => 2,
+                 className => 'feature2',
+               },
+               '--clientConfig option seems to work'
+             ) or diag explain $read_json->('trackList.json');
+
+    #system "find $tempdir";
+}
+
+{#   diag "running on single_au9_gene.gff3, testing --type filtering";
+
+    my $tempdir = tempdir();
+    dircopy( 'tests/data/AU9', $tempdir );
+
+    run_with (
+        '--out' => $tempdir,
+        '--gff' => "tests/data/AU9/single_au9_gene.gff3",
+        '--trackLabel' => 'AU_mRNA',
+        '--key' => 'AU mRNA',
+        '--type' => 'mRNA',
+        '--autocomplete' => 'all',
+        '--cssClass' => 'transcript',
+        '--getPhase',
+        '--getSubfeatures',
+        );
+
+    #system "find $tempdir";
+
+    my $read_json = sub { JsonGenerator::readJSON( catfile( $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' )
+       or diag explain $cds_trackdata;
+    is( scalar @{$cds_trackdata->{intervals}{nclist}[0][9]}, 7, 'mRNA has 7 subfeatures' );
+}
 
 done_testing;