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:
- tests/tripal_chado/loaders/GFF3ImporterTest.php
