def test_get_files_valid_dir_invalid_id(self):
valid_dir = path.join(path_to_module, "fake_ngs_data")
invalid_sample_id = "-1~"
fastq_files = get_all_fastq_files(valid_dir)
file_list = get_pair_files(fastq_files, invalid_sample_id)
self.assertEqual(len(file_list), 0)
def test_get_files_invalid_dir_valid_id(self):
invalid_dir = "+/not a directory/+"
valid_sample_id = "01-1111"
with self.assertRaises(OSError) as context:
fastq_files = get_all_fastq_files(invalid_dir)
get_pair_files(fastq_files, valid_sample_id)
self.assertTrue("Invalid directory" in str(context.exception))
def test_common_prefix_sample_names(self):
sheet_file = path.join(path_to_module, "testCommonPrefixSampleName",
"SampleSheet.csv")
sample_list = parse_samples(sheet_file)
fastq_files = get_all_fastq_files(path.join(path_to_module, "testCommonPrefixSampleName"))
for sample in sample_list:
sample_id = sample['sequencerSampleId']
file_list = get_pair_files(fastq_files, sample_id)
self.assertEquals(len(file_list), 2)
def test_get_files_valid_dir_valid_id(self):
valid_dir = path.join(path_to_module, "fake_ngs_data")
valid_sample_id = "01-1111"
fastq_files = get_all_fastq_files(valid_dir)
file_list = get_pair_files(fastq_files, valid_sample_id)
correct_list = [
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "01-1111_S1_L001_R1_001.fastq.gz"),
path.join(path_to_module, "fake_ngs_data", "Data", "Intensities",
"BaseCalls", "01-1111_S1_L001_R2_001.fastq.gz")]
self.assertEqual(correct_list, file_list)
def test_complete_parse_samples(self):
sheet_file = path.join(path_to_module, "fake_ngs_data",
"SampleSheet.csv")
data_dir = path.join(path_to_module, "fake_ngs_data")
sample_list = complete_parse_samples(sheet_file)
self.assertEqual(len(sample_list), 3)
required_data_headers = [
"sampleName",
"description",
"sequencerSampleId",
"sampleProject"]
seq_file_headers = [
"index",
"I7_Index_ID",
"Sample_Well",
"Sample_Plate",
"index2",
"I5_Index_ID"]
for sample in sample_list:
# sample only has the 4 required data headers as keys
self.assertEqual(
len(sample.get_dict().keys()), len(required_data_headers))
# check if all values in required_data_headers are found in the
# sample's dictionary keys
self.assertTrue(
all([data_header in sample.get_dict().keys() for data_header in
required_data_headers]))
# check if all values in seq_file_headers are found in the Sequence
# File properties dict /Sample metadata
self.assertTrue(
all([data_header in sample.get_sample_metadata().keys()
for data_header in seq_file_headers]))
self.assertEqual(len(sample.get_files()), 2)
fastq_files = get_all_fastq_files(data_dir)
pf_list = get_pair_files(fastq_files, sample.get_id())
self.assertEqual(pf_list, sample.get_files())