def test_fastq_gz_format_validate_mixed_case(self):
filepath = self.get_data_path('mixed-case.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValueError, 'FastqGzFormat'):
format.validate()
def test_partial_record(self):
filepath = self.get_data_path('partial-record.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'sequence.*1'):
format.validate()
def test_fastq_gz_format_validate_positive(self):
filepath = self.get_data_path('Human-Kneecap_S1_L001_R1_001.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
format.validate()
def test_invalid_record_sep(self):
filepath = self.get_data_path('invalid-sep.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'separator.*11'):
format.validate()
def test_invalid_quality_score_length(self):
filepath = self.get_data_path('invalid-quality.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'length.*9'):
format.validate()
def test_validate_uncompressed(self):
filepath = self.get_data_path('Human-Kneecap_S1_L001_R1_001.fastq')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'uncompressed'):
format.validate()
def test_incomplete_record_sequence(self):
filepath = self.get_data_path('incomplete-sequence.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'sequence.*9'):
format.validate()
def test_validate_negative(self):
filepath = self.get_data_path('not-fastq.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'Header.*1'):
format.validate()
def test_validate_mixed_case(self):
filepath = self.get_data_path('mixed-case.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'Lowercase.*2'):
format.validate()
def test_validate_uncompressed(self):
filepath = self.get_data_path('Human-Kneecap_S1_L001_R1_001.fastq')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'uncompressed'):
format.validate()
def test_validate_positive(self):
filepath = self.get_data_path('Human-Kneecap_S1_L001_R1_001.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
format.validate()
def test_validate_negative(self):
filepath = self.get_data_path('not-fastq.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'Header.*1'):
format.validate()
def test_partial_record(self):
filepath = self.get_data_path('partial-record.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'sequence.*1'):
format.validate()
def test_invalid_quality_score_length(self):
filepath = self.get_data_path('invalid-quality.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'length.*9'):
format.validate()
def test_invalid_record_sep(self):
filepath = self.get_data_path('invalid-sep.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'separator.*11'):
format.validate()
def test_incomplete_record_sequence(self):
filepath = self.get_data_path('incomplete-sequence.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
with self.assertRaisesRegex(ValidationError, 'sequence.*9'):
format.validate()