def analyze_one(soft_file, isamp, interested_organisms):
"""analyze a single soft_file"""
if not filename_check(soft_file):
return
s_series = parse(soft_file, interested_organisms)
# s_series should be in the list of series that are interested by the
# collaborator
if not s_series.name in isamp.keys():
logger.warning('{0} from {1} does not appear in '
'isamp'.format(s_series.name, soft_file))
return
return intersect(s_series, isamp)
def analyze_one(soft_file, isamp, interested_organisms):
"""analyze a single soft_file"""
if not filename_check(soft_file):
return
s_series = parse(soft_file, interested_organisms)
# s_series should be in the list of series that are interested by the
# collaborator
if not s_series.name in isamp.keys():
logger.warning('{0} from {1} does not appear in '
'isamp'.format(s_series.name, soft_file))
return
return intersect(s_series, isamp)
def test_parse(self):
m = mock.mock_open()
with mock.patch('rsempipeline.parsers.soft_parser.open', m):
m.return_value.__iter__.return_value = settings.GSE43770_FAMILY_SOFT_SUBSET_CONTENT.splitlines()
series = soft_parser.parse('GSE43770_family.soft.subset',
['H**o sapiens', 'Mus musculus'])
m.assert_called_once_with('GSE43770_family.soft.subset', 'rb')
self.assertEqual(series.name, 'GSE43770')
self.assertEqual([__.name for __ in series.passed_samples],
['GSM1070765', 'GSM1070766'])
self.assertEqual([__.index for __ in series.passed_samples],
[1, 2])
self.assertEqual([__.name for __ in series.samples],
['GSM1070765', 'GSM1070766', 'GSM1070767'])
self.assertEqual([__.index for __ in series.samples],
[1, 2, 0]) # 0 mean unindexed
def test_parse(self):
m = mock.mock_open()
with mock.patch('rsempipeline.parsers.soft_parser.open', m):
m.return_value.__iter__.return_value = settings.GSE43770_FAMILY_SOFT_SUBSET_CONTENT.splitlines(
)
series = soft_parser.parse('GSE43770_family.soft.subset',
['H**o sapiens', 'Mus musculus'])
m.assert_called_once_with('GSE43770_family.soft.subset', 'rb')
self.assertEqual(series.name, 'GSE43770')
self.assertEqual([__.name for __ in series.passed_samples],
['GSM1070765', 'GSM1070766'])
self.assertEqual([__.index for __ in series.passed_samples],
[1, 2])
self.assertEqual([__.name for __ in series.samples],
['GSM1070765', 'GSM1070766', 'GSM1070767'])
self.assertEqual([__.index for __ in series.samples],
[1, 2, 0]) # 0 mean unindexed
