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Tests\GFF3ImporterTest Class Reference
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Public Member Functions

 testGFFImporter ()
 
 testGFFImporterUnescapedTagWithComma ()
 
 testGFFImporterTagAliasVerification ()
 
 testGFFImporterTagParentVerification ()
 
 testGFFImporterEscapedTagValueWithEncodedCharacter ()
 
 testGFFImporterUnescapedTagValueWithComma ()
 
 testGFFImporterSeqidWithInvalidCharacter ()
 
 testGFFImporterUnescapedWhitespaceID ()
 
 testGFFImporterRightArrowID ()
 
 testGFFImporterDuplicateIDsExceptionCheck ()
 
 testGFFImporterInvalidStartEnd ()
 
 testGFFImporterScoreTest ()
 
 testGFFImporterInvalidStrandTest ()
 
 testGFFImporterStrandTest ()
 
 testGFFImporterPhaseTest ()
 
 testGFFImporterInvalidPhaseNumberTest ()
 
 testGFFImporterInvalidPhaseCharacterTest ()
 
 testGFFImporterAttributeFeature ()
 
 testGFFImporterAttributeAlias ()
 
 testGFFImporterAttributeDbxref ()
 
 testGFFImporterAttributeOntology ()
 
 testGFFImporterAttributeParent ()
 
 testGFFImporterAttributeTarget ()
 
 testGFFImporterAttributeProperty ()
 
 testGFFImporterAttributeDerivesFrom ()
 
 testGFFImporterAttributeFastas ()
 
 testGFFPolypeptide ()
 
 testGFFNoProteinOption ()
 
 testGFFImporterLoadsExplicitProteins ()
 
 testGFFImporterCreatesLandmarkFromGFFDefinition ()
 

Member Function Documentation

◆ testGFFImporter()

Tests\GFF3ImporterTest::testGFFImporter ( )

Confirm basic GFF importer functionality.

@group gff

◆ testGFFImporterAttributeAlias()

Tests\GFF3ImporterTest::testGFFImporterAttributeAlias ( )

Ensures the feature alias is loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeDbxref()

Tests\GFF3ImporterTest::testGFFImporterAttributeDbxref ( )

Ensures that the dbxref records are loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeDerivesFrom()

Tests\GFF3ImporterTest::testGFFImporterAttributeDerivesFrom ( )

Ensure derives from information loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeFastas()

Tests\GFF3ImporterTest::testGFFImporterAttributeFastas ( )

Ensure FASTA information loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeFeature()

Tests\GFF3ImporterTest::testGFFImporterAttributeFeature ( )

Ensures that the feature record is loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeOntology()

Tests\GFF3ImporterTest::testGFFImporterAttributeOntology ( )

Ensures ontology term records loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeParent()

Tests\GFF3ImporterTest::testGFFImporterAttributeParent ( )

Ensures feature parent record loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeProperty()

Tests\GFF3ImporterTest::testGFFImporterAttributeProperty ( )

Ensure properties loaded correctly into chado.

@group gff

◆ testGFFImporterAttributeTarget()

Tests\GFF3ImporterTest::testGFFImporterAttributeTarget ( )

Ensure target record loaded correctly into chado.

@group gff

◆ testGFFImporterCreatesLandmarkFromGFFDefinition()

Tests\GFF3ImporterTest::testGFFImporterCreatesLandmarkFromGFFDefinition ( )

The GFF importer should create new landmarks if they are defined in the GFF file and the corresponding checkbox is checked, or fail if not checked.

@group gff @ticket 1324

regexps for mRNA and protein.

◆ testGFFImporterDuplicateIDsExceptionCheck()

Tests\GFF3ImporterTest::testGFFImporterDuplicateIDsExceptionCheck ( )

Run the GFF loader on gff_duplicate_ids.gff for testing.

This tests whether the GFF loader detects duplicate IDs which makes a GFF file invalid since IDs should be unique. The GFF loader should throw and exception which this test checks for

◆ testGFFImporterEscapedTagValueWithEncodedCharacter()

Tests\GFF3ImporterTest::testGFFImporterEscapedTagValueWithEncodedCharacter ( )

Run the GFF loader on gff_tagvalue_unescaped_character.gff for testing.

This tests whether the GFF loader adds IDs that contain a comma. The GFF loader should allow it

◆ testGFFImporterInvalidPhaseCharacterTest()

Tests\GFF3ImporterTest::testGFFImporterInvalidPhaseCharacterTest ( )

Run the GFF loader on gff_phase_invalid_character.gff for testing.

This tests whether the GFF loader interprets the phase values correctly for CDS rows when a character outside of the range 0,1,2 is specified.

◆ testGFFImporterInvalidPhaseNumberTest()

Tests\GFF3ImporterTest::testGFFImporterInvalidPhaseNumberTest ( )

Run the GFF loader on gff_phase_invalid_number.gff for testing.

This tests whether the GFF loader interprets the phase values correctly for CDS rows when a number outside of the range 0,1,2 is specified.

◆ testGFFImporterInvalidStartEnd()

Tests\GFF3ImporterTest::testGFFImporterInvalidStartEnd ( )

Run the GFF loader on gff_invalidstartend.gff for testing.

This tests whether the GFF loader fixes start end values

◆ testGFFImporterInvalidStrandTest()

Tests\GFF3ImporterTest::testGFFImporterInvalidStrandTest ( )

Run the GFF loader on gff_strand.gff for testing.

This tests whether the GFF loader interprets the strand values

◆ testGFFImporterLoadsExplicitProteins()

Tests\GFF3ImporterTest::testGFFImporterLoadsExplicitProteins ( )

The GFF importer should still create explicitly defined proteins if skip_protein is true.

@group gff @ticket 77

regexps for mRNA and protein.

◆ testGFFImporterPhaseTest()

Tests\GFF3ImporterTest::testGFFImporterPhaseTest ( )

Run the GFF loader on gff_phase.gff for testing.

This tests whether the GFF loader interprets the phase values correctly for CDS rows.

◆ testGFFImporterRightArrowID()

Tests\GFF3ImporterTest::testGFFImporterRightArrowID ( )

Run the GFF loader on gff_rightarrow_ids.gff for testing.

This tests whether the GFF loader fails if ID contains
arrow >. It should not fail.

◆ testGFFImporterScoreTest()

Tests\GFF3ImporterTest::testGFFImporterScoreTest ( )

Run the GFF loader on gff_score.gff for testing.

This tests whether the GFF loader interprets the score values

◆ testGFFImporterSeqidWithInvalidCharacter()

Tests\GFF3ImporterTest::testGFFImporterSeqidWithInvalidCharacter ( )

Run the GFF loader on gff_seqid_invalid_character.gff for testing. Seqids seem to also be called landmarks within GFF loader. This tests whether the GFF loader has any issues with characters like
single quotes.

◆ testGFFImporterStrandTest()

Tests\GFF3ImporterTest::testGFFImporterStrandTest ( )

Run the GFF loader on gff_strand.gff for testing.

This tests whether the GFF loader interprets the strand values

◆ testGFFImporterTagAliasVerification()

Tests\GFF3ImporterTest::testGFFImporterTagAliasVerification ( )

Run the GFF loader on small_gene.gff for testing.

This tests whether the GFF loader adds Alias attributes The GFF loader should allow it

◆ testGFFImporterTagParentVerification()

Tests\GFF3ImporterTest::testGFFImporterTagParentVerification ( )

Run the GFF loader on gff_tag_parent_verification.gff for testing.

This tests whether the GFF loader adds Parent attributes The GFF loader should allow it

◆ testGFFImporterUnescapedTagValueWithComma()

Tests\GFF3ImporterTest::testGFFImporterUnescapedTagValueWithComma ( )

Run the GFF loader on gff_tagvalue_unescaped_character.gff for testing.

This tests whether the GFF loader adds IDs that contain a comma. The GFF loader should allow it

◆ testGFFImporterUnescapedTagWithComma()

Tests\GFF3ImporterTest::testGFFImporterUnescapedTagWithComma ( )

Run the GFF loader on gff_tag_unescaped_character.gff for testing.

This tests whether the GFF loader adds IDs that contain a comma. The GFF loader should allow it

◆ testGFFImporterUnescapedWhitespaceID()

Tests\GFF3ImporterTest::testGFFImporterUnescapedWhitespaceID ( )

Run the GFF loader on gff_unescaped_ids.gff for testing.

This tests whether the GFF loader adds IDs that contain whitespaces. The GFF loader should allow it

◆ testGFFNoProteinOption()

Tests\GFF3ImporterTest::testGFFNoProteinOption ( )

Add a skip protein option. Test that when checked, implicit proteins are not created, but that they are created when unchecked.

@group gff @ticket 77

regexps for mRNA and protein.

◆ testGFFPolypeptide()

Tests\GFF3ImporterTest::testGFFPolypeptide ( )

Test that when checked, explicit proteins are created when specified within the GFF file. Explicit proteins will not respect the skip_protein argument and will therefore be added to the database.

@group gff @ticket 77


The documentation for this class was generated from the following file: