def _write_empty_fastq_to_mux_barcode_in_seq_fmt(seqs_dir_fmt):
fastq = FastqGzFormat()
with gzip.open(str(fastq), 'w') as fh:
fh.write(b'')
# PAIRED-END
if isinstance(seqs_dir_fmt, MultiplexedPairedEndBarcodeInSequenceDirFmt):
seqs_dir_fmt.forward_sequences.write_data(fastq, FastqGzFormat)
seqs_dir_fmt.reverse_sequences.write_data(fastq, FastqGzFormat)
# SINGLE-END
else:
seqs_dir_fmt.file.write_data(fastq, FastqGzFormat)
def setUp(self):
super().setUp()
self.fastq_fp = \
self.get_data_path('forward.fastq.gz')
self.fastq = FastqGzFormat(self.fastq_fp, mode='r')
self.seqs_dir_fmt = MultiplexedSingleEndBarcodeInSequenceDirFmt()
self.seqs_dir_fmt.file.write_data(self.fastq, FastqGzFormat)
self.barcode_series = pd.Series(['A', 'G'],
index=['sample_a', 'sample_b'])
self.per_sample_dir_fmt = SingleLanePerSampleSingleEndFastqDirFmt()
self.untrimmed_dir_fmt = MultiplexedSingleEndBarcodeInSequenceDirFmt()
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_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_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_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_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 _write_empty_fastq_to_mux_barcode_in_seq_fmt(seqs_dir_fmt):
fastq = FastqGzFormat()
with gzip.open(str(fastq), 'w') as fh:
fh.write(b'')
seqs_dir_fmt.file.write_data(fastq, FastqGzFormat)
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_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_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_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()
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_validate_positive(self):
filepath = self.get_data_path('Human-Kneecap_S1_L001_R1_001.fastq.gz')
format = FastqGzFormat(filepath, mode='r')
format.validate()
