def test_get_column_data(self):
"""
Test: Assert array equals when getting column data
"""
try:
log.info(TestFilteredSummaryReader.test_count_records.__doc__)
fsr = FilteredSummaryReader(
os.path.join(BaseTestCase.get_data_dir(), 'loading',
'filtered_summary_small.csv'))
fsr.load()
ri_exp = [
'm120128_025832_42129_c100277632550000001523007907041250_s2_p0/0',
'm120128_025832_42129_c100277632550000001523007907041250_s2_p0/1'
]
ri_act = []
data = fsr.data_as_numpy_array()
for row in data:
ri_act.append(row['ReadId'])
self.assertSequenceEqual(ri_exp, ri_act)
except:
log.error(traceback.format_exc())
raise
def test_count_records(self):
"""
Test: Count num csv records
"""
try:
log.info(TestFilteredSummaryReader.test_count_records.__doc__)
fsr = FilteredSummaryReader(os.path.join(BaseTestCase.get_data_dir(), 'loading', 'filtered_summary_small.csv'))
fsr.load()
self.assertEqual(2, fsr.num_records)
except:
log.error(traceback.format_exc())
raise
def test_num_reads(self):
"""
Test: get num reads from csv
"""
try:
log.info(TestFilteredSummaryReader.test_num_reads.__doc__)
fsr = FilteredSummaryReader(
os.path.join(BaseTestCase.get_data_dir(), 'loading',
'filtered_summary_small.csv'))
fsr.load()
self.assertEqual(1, fsr.num_reads)
except:
log.error(traceback.format_exc())
raise
def test_get_column_data(self):
"""
Test: Assert array equals when getting column data
"""
try:
log.info(TestFilteredSummaryReader.test_count_records.__doc__)
fsr = FilteredSummaryReader(os.path.join(BaseTestCase.get_data_dir(), 'loading', 'filtered_summary_small.csv'))
fsr.load()
ri_exp = ['m120128_025832_42129_c100277632550000001523007907041250_s2_p0/0',
'm120128_025832_42129_c100277632550000001523007907041250_s2_p0/1']
ri_act = []
data = fsr.data_as_numpy_array()
for row in data:
ri_act.append(row['ReadId'])
self.assertSequenceEqual(ri_exp, ri_act)
except:
log.error(traceback.format_exc())
raise
def _create_adapter_report(self):
"""
Creates and returns an Adapter Report
"""
from pbreports.report.adapter import make_adapter_report
from test_pbreports_report_adapters import DataCache as d
BaseTestCase.setUpClass()
d.data_dir = BaseTestCase.get_data_dir()
log.info(
'Creating adapter report using datadir {d}'.format(d=d.data_dir))
fofn = os.path.join(self._output_dir, 'test.fofn')
d.write_fofn(fofn)
dpi = 60
dumpdata = False
output_json = os.path.join(self._output_dir, 'adapter.json')
make_adapter_report(fofn, 'adapter.json', self._output_dir, dpi,
dumpdata)
return self._deserialize_report(output_json)
def _create_adapter_report(self):
"""
Creates and returns an Adapter Report
"""
from pbreports.report.adapter import make_adapter_report
from test_pbreports_report_adapters import DataCache as d
BaseTestCase.setUpClass()
d.data_dir = BaseTestCase.get_data_dir()
log.info(
'Creating adapter report using datadir {d}'.format(d=d.data_dir))
fofn = os.path.join(self._output_dir, 'test.fofn')
d.write_fofn(fofn)
dpi = 60
dumpdata = False
output_json = os.path.join(self._output_dir, 'adapter.json')
make_adapter_report(
fofn, 'adapter.json', self._output_dir, dpi, dumpdata)
return self._deserialize_report(output_json)
