def test_slanepsample_single_end_fastq_dir_fmt_validate_positive(self):
filenames = ('single_end_data/MANIFEST', 'metadata.yml',
'Human-Kneecap_S1_L001_R1_001.fastq.gz')
for filename in filenames:
filepath = self.get_data_path(filename)
shutil.copy(filepath, self.temp_dir.name)
format = SingleLanePerSampleSingleEndFastqDirFmt(
self.temp_dir.name, mode='r')
format.validate()
def test_slanepsample_single_end_fastq_dir_fmt_validate_positive(self):
filenames = ('single_end_data/MANIFEST', 'metadata.yml',
'Human-Kneecap_S1_L001_R1_001.fastq.gz')
for filename in filenames:
filepath = self.get_data_path(filename)
shutil.copy(filepath, self.temp_dir.name)
format = SingleLanePerSampleSingleEndFastqDirFmt(self.temp_dir.name,
mode='r')
format.validate()
def test_slanepsample_single_end_fastq_dir_fmt_validate_negative(self):
filenames = ('single_end_data/MANIFEST', 'metadata.yml',
'not-fastq.fastq.gz')
for filename in filenames:
filepath = self.get_data_path(filename)
shutil.copy(filepath, self.temp_dir.name)
format = SingleLanePerSampleSingleEndFastqDirFmt(
self.temp_dir.name, mode='r')
with self.assertRaisesRegex(ValueError, 'SingleLanePerSampleSingle'):
format.validate()
def test_slanepsample_single_end_fastq_dir_fmt_validate_negative(self):
filenames = ('single_end_data/MANIFEST', 'metadata.yml',
'not-fastq.fastq.gz')
for filename in filenames:
filepath = self.get_data_path(filename)
shutil.copy(filepath, self.temp_dir.name)
format = SingleLanePerSampleSingleEndFastqDirFmt(self.temp_dir.name,
mode='r')
with self.assertRaisesRegex(ValueError, 'SingleLanePerSampleSingle'):
format.validate()
def test_slanepsample_single_end_fastq_dir_fmt_validate_bad_paired(self):
filenames = ('paired_end_data/MANIFEST', 'metadata.yml',
'Human-Kneecap_S1_L001_R1_001.fastq.gz',
'paired_end_data/Human-Kneecap_S1_L001_R2_001.fastq.gz')
for filename in filenames:
filepath = self.get_data_path(filename)
shutil.copy(filepath, self.temp_dir.name)
format = SingleLanePerSampleSingleEndFastqDirFmt(self.temp_dir.name,
mode='r')
with self.assertRaisesRegex(ValidationError, 'Forward and reverse'):
format.validate()
def test_slanepsample_single_end_fastq_dir_fmt_validate_bad_paired(self):
filenames = ('paired_end_data/MANIFEST', 'metadata.yml',
'Human-Kneecap_S1_L001_R1_001.fastq.gz',
'paired_end_data/Human-Kneecap_S1_L001_R2_001.fastq.gz')
for filename in filenames:
filepath = self.get_data_path(filename)
shutil.copy(filepath, self.temp_dir.name)
format = SingleLanePerSampleSingleEndFastqDirFmt(
self.temp_dir.name, mode='r')
with self.assertRaisesRegex(ValidationError, 'Forward and reverse'):
format.validate()
