def test_combine_metrics(self):
"""Test combining metrics"""
amsa = AMa.category()
mlist = list(zip([DMa],[IMa],[amsa],[HMa]))
colnames = [c for sublist in [m.metrics.colnames for mtup in mlist for m in mtup] for c in sublist]
cnt = Counter(colnames)
# Merge colnames
pm = combine_metrics(mlist)
self.assertEqual((len(cnt)), pm.metrics.dim[1])
# Make colnames unique
pm = combine_metrics(mlist, uniquify=True)
self.assertEqual((len(colnames)), pm.metrics.dim[1])
def setUp():
"""Set up test fixtures"""
global mlist, Sample, pm
Sample = namedtuple('Sample', ['sample_id', 'project_id', 'pm'])
metricsroot = os.path.join(os.path.abspath(os.curdir),
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 = [x for x in metricsfiles if x.endswith('align_metrics')]
hs_metrics = [x for x in metricsfiles if x.endswith('hs_metrics')]
insert_metrics = [x for x in metricsfiles if x.endswith('insert_metrics')]
dup_metrics = [x for x in metricsfiles if x.endswith('dup_metrics')]
mlist =(list(
zip(
[AlignMetrics(filename=x).category() for x in align_metrics],
[InsertMetrics(filename=x) for x in insert_metrics],
[DuplicationMetrics(filename=x) for x in dup_metrics],
[HsMetrics(filename=x) for x in hs_metrics]
)
))
pm = combine_metrics(mlist)
def test_combine_multiple_metrics(self):
"""Test combining multiple metrics"""
mlist =(list(
zip(
[AlignMetrics(filename=x).category() for x in align_metrics],
[InsertMetrics(filename=x) for x in insert_metrics],
[DuplicationMetrics(filename=x) for x in dup_metrics],
[HsMetrics(filename=x) for x in hs_metrics]
)
))
pm = combine_metrics(mlist)
self.assertTupleEqual(pm.metrics.dim, (2,91))
self.assertListEqual(pm.summary(raw=True).split("\n")[1].split("\t")[:25], [v for k,v in AMa.metrics.data[2].items()])