def gen_all_samples_from_soft_and_isamp(soft_files, isamp_file_or_str, config):
"""
:param isamp: e.g. mannually prepared interested sample file
(e.g. GSE_species_GSM.csv) or isamp_str as specified on the command
:type isamp: a dict with key and value as listing of strings, not Sample
instances
"""
# IMPORTANT NOTE: for historical reason, soft files parsed does not return
# dict as get_isamp
isamp = get_isamp(isamp_file_or_str)
log_isamp(isamp_file_or_str, isamp)
# a list, of Sample instances resultant of intersection
intersected_samples = []
for soft_file in soft_files:
soft_samples = analyze_one(soft_file, isamp, config['INTERESTED_ORGANISMS'])
if soft_samples:
intersected_samples.extend(soft_samples)
num_inter_samp = len(intersected_samples)
sanity_check(calc_num_isamp(isamp), num_inter_samp)
return intersected_samples
def gen_all_samples_from_soft_and_isamp(soft_files, isamp_file_or_str, config):
"""
:param isamp: e.g. mannually prepared interested sample file
(e.g. GSE_species_GSM.csv) or isamp_str as specified on the command
:type isamp: a dict with key and value as listing of strings, not Sample
instances
"""
# IMPORTANT NOTE: for historical reason, soft files parsed does not return
# dict as get_isamp
isamp = get_isamp(isamp_file_or_str)
log_isamp(isamp_file_or_str, isamp)
# a list, of Sample instances resultant of intersection
intersected_samples = []
for soft_file in soft_files:
soft_samples = analyze_one(soft_file, isamp,
config['INTERESTED_ORGANISMS'])
if soft_samples:
intersected_samples.extend(soft_samples)
num_inter_samp = len(intersected_samples)
sanity_check(calc_num_isamp(isamp), num_inter_samp)
return intersected_samples
def test_get_isamp_from_str(self, mock_exists, mock_gen_isamp_from_csv):
mock_exists.return_value = False
self.assertEqual(isamp_parser.get_isamp('GSE1 GSM1'),
{'GSE1': ['GSM1']})
self.assertFalse(mock_gen_isamp_from_csv.called)
def test_get_isamp_from_csv(self, mock_exists, mock_gen_isamp_from_csv,
mock_gen_isamp_from_str):
mock_exists.return_value = True
isamp_parser.get_isamp('GSE_species_GSM.csv')
mock_gen_isamp_from_csv.called_once_with('GSE_species_GSM.csv')
self.assertFalse(mock_gen_isamp_from_str.called)
def test_get_isamp_from_str(self, mock_exists, mock_gen_isamp_from_csv):
mock_exists.return_value = False
self.assertEqual(isamp_parser.get_isamp('GSE1 GSM1'), {'GSE1': ['GSM1']})
self.assertFalse(mock_gen_isamp_from_csv.called)
def test_get_isamp_from_csv(self, mock_exists, mock_gen_isamp_from_csv,
mock_gen_isamp_from_str):
mock_exists.return_value = True
isamp_parser.get_isamp('GSE_species_GSM.csv')
mock_gen_isamp_from_csv.called_once_with('GSE_species_GSM.csv')
self.assertFalse(mock_gen_isamp_from_str.called)
