def test_picard_read_metrics(self):
"""Test function _read_picard_metrics"""
(metrics, hist) = _read_picard_metrics(align_metrics[0])
self.assertIsNone(hist)
self.assertEqual(len(metrics), 4)
(metrics, hist) = _read_picard_metrics(insert_metrics[0])
self.assertListEqual(sorted(hist[0]), sorted(['insert_size', 'All_Reads.fr_count']))
self.assertEqual(metrics[1][0], 156)
def setUp():
"""Set up test fixtures for metrics test"""
global PM, PH, AMa, IMa, DMa, HMa, AMf, IMf, DMf, HMf, align_metrics, dup_metrics, insert_metrics, hs_metrics, alnmet, insmet, dupmet, hsmet, inshist, duphist, Adf, Idf, Idfh, Ddf, Ddfh, Hdf
metricsroot = os.path.join(os.path.abspath(os.path.dirname(__file__)),
os.pardir, 'data', 'metrics', 'J.Doe_00_01')
metricsfiles = []
for root, dirs, files in os.walk(metricsroot):
metricsfiles += [os.path.join(root, x) for x in files if x.endswith('metrics')]
align_metrics = sorted([x for x in metricsfiles if x.endswith('align_metrics')])
hs_metrics = sorted([x for x in metricsfiles if x.endswith('hs_metrics')])
insert_metrics = sorted([x for x in metricsfiles if x.endswith('insert_metrics')])
dup_metrics = sorted([x for x in metricsfiles if x.endswith('dup_metrics')])
(alnmet, _) = _read_picard_metrics(align_metrics[0])
(insmet, inshist) = _read_picard_metrics(insert_metrics[0])
(hsmet, _) = _read_picard_metrics(hs_metrics[0])
(dupmet, duphist) = _read_picard_metrics(dup_metrics[0])
PM = PicardMetrics(identifier="PM", filename=align_metrics[0])
PH = PicardHistMetrics(identifier="PH", filename=insert_metrics[0])
AMf = AlignMetrics(identifier="AM", filename=align_metrics[0])
IMf = InsertMetrics(identifier="IM", filename=insert_metrics[0])
HMf = HsMetrics(identifier="HM", filename=hs_metrics[0])
DMf = DuplicationMetrics(identifier="DM", filename=dup_metrics[0])
AMa = AlignMetrics(*alnmet, identifier="AM")
IMa = InsertMetrics(*insmet, hist=inshist, identifier="IM")
HMa = HsMetrics(*hsmet, identifier="HM")
DMa = DuplicationMetrics(*dupmet, hist=duphist, identifier="DM")
Adf = DataFrame(*alnmet)
Idf = DataFrame(*insmet)
Idfh = DataFrame(*inshist)
Ddf = DataFrame(*dupmet)
Ddfh = DataFrame(*duphist)
Hdf = DataFrame(*hsmet)