def test_04_chromosome_batch(self):
if ONLY and not "04" in ONLY:
return
if CHKTIME:
t0 = time()
test_chr = Chromosome(name="Test Chromosome",
experiment_resolutions=[20000] * 3,
experiment_hic_data=[
PATH + "/20Kb/chrT/chrT_A.tsv",
PATH + "/20Kb/chrT/chrT_D.tsv",
PATH + "/20Kb/chrT/chrT_C.tsv"
],
experiment_names=["exp1", "exp2", "exp3"],
silent=True)
test_chr.find_tad(["exp1", "exp2", "exp3"],
batch_mode=True,
verbose=False,
silent=True)
tads = test_chr.get_experiment("batch_exp1_exp2_exp3").tads
found = [tads[t]["end"] for t in tads if tads[t]["score"] > 0]
# Values obtained with square root normalization.
#self.assertEqual([3.0, 8.0, 16.0, 21.0, 28.0, 35.0, 43.0,
# 49.0, 61.0, 66.0, 75.0, 89.0, 94.0, 99.0], found)
self.assertEqual([
3.0, 14.0, 19.0, 33.0, 43.0, 49.0, 61.0, 66.0, 71.0, 89.0, 94.0,
99.0
], found)
if CHKTIME:
print "4", time() - t0
def test_04_chromosome_batch(self):
if ONLY and ONLY != "04":
return
if CHKTIME:
t0 = time()
test_chr = Chromosome(
name="Test Chromosome",
experiment_resolutions=[20000] * 3,
experiment_hic_data=[
PATH + "/20Kb/chrT/chrT_A.tsv",
PATH + "/20Kb/chrT/chrT_D.tsv",
PATH + "/20Kb/chrT/chrT_C.tsv",
],
experiment_names=["exp1", "exp2", "exp3"],
silent=True,
)
test_chr.find_tad(["exp1", "exp2", "exp3"], batch_mode=True, verbose=False, silent=True)
tads = test_chr.get_experiment("batch_exp1_exp2_exp3").tads
found = [tads[t]["end"] for t in tads if tads[t]["score"] > 0]
# Values obtained with square root normalization.
# self.assertEqual([3.0, 8.0, 16.0, 21.0, 28.0, 35.0, 43.0,
# 49.0, 61.0, 66.0, 75.0, 89.0, 94.0, 99.0], found)
self.assertEqual([3.0, 14.0, 19.0, 33.0, 43.0, 49.0, 61.0, 66.0, 71.0, 89.0, 94.0, 99.0], found)
if CHKTIME:
print "4", time() - t0
def test_04_chromosome_batch(self):
if ONLY and ONLY != '04':
return
if CHKTIME:
t0 = time()
test_chr = Chromosome(name='Test Chromosome',
experiment_resolutions=[20000]*3,
experiment_hic_data=[
PATH + '/20Kb/chrT/chrT_A.tsv',
PATH + '/20Kb/chrT/chrT_D.tsv',
PATH + '/20Kb/chrT/chrT_C.tsv'],
experiment_names=['exp1', 'exp2', 'exp3'],
silent=True)
test_chr.find_tad(['exp1', 'exp2', 'exp3'], batch_mode=True,
verbose=False, silent=True)
tads = test_chr.get_experiment('batch_exp1_exp2_exp3').tads
found = [tads[t]['end'] for t in tads if tads[t]['score'] > 0]
# Values obtained with square root normalization.
#self.assertEqual([3.0, 8.0, 16.0, 21.0, 28.0, 35.0, 43.0,
# 49.0, 61.0, 66.0, 75.0, 89.0, 94.0, 99.0], found)
self.assertEqual([3.0, 14.0, 19.0, 33.0, 43.0, 49.0, 61.0, 66.0,
71.0, 89.0, 94.0, 99.0], found)
if CHKTIME:
print '4', time() - t0
def test_04_chromosome_batch(self):
if ONLY and ONLY != '04':
return
if CHKTIME:
t0 = time()
test_chr = Chromosome(name='Test Chromosome',
experiment_resolutions=[20000]*3,
experiment_hic_data=[
PATH + '/20Kb/chrT/chrT_A.tsv',
PATH + '/20Kb/chrT/chrT_D.tsv',
PATH + '/20Kb/chrT/chrT_C.tsv'],
experiment_names=['exp1', 'exp2', 'exp3'],
silent=True)
test_chr.find_tad(['exp1', 'exp2', 'exp3'], batch_mode=True,
verbose=False, silent=True)
tads = test_chr.get_experiment('batch_exp1_exp2_exp3').tads
found = [tads[t]['end'] for t in tads if tads[t]['score'] > 0]
# Values obtained with square root normalization.
#self.assertEqual([3.0, 8.0, 16.0, 21.0, 28.0, 35.0, 43.0,
# 49.0, 61.0, 66.0, 75.0, 89.0, 94.0, 99.0], found)
self.assertEqual([3.0, 14.0, 19.0, 33.0, 43.0, 49.0, 61.0, 66.0,
71.0, 89.0, 94.0, 99.0], found)
if CHKTIME:
print '4', time() - t0
def test_04_chromosome_batch(self):
test_chr = Chromosome(name='Test Chromosome',
experiment_resolutions=[20000]*3,
experiment_hic_data=['20Kb/chrT/chrT_A.tsv',
'20Kb/chrT/chrT_D.tsv',
'20Kb/chrT/chrT_C.tsv'],
experiment_names=['exp1', 'exp2', 'exp3'])
test_chr.find_tad(['exp1', 'exp2', 'exp3'], batch_mode=True,
verbose=False)
tads = test_chr.get_experiment('batch_exp1_exp2_exp3').tads
found = [tads[t]['end'] for t in tads if tads[t]['score'] > 0]
self.assertEqual([3.0, 8.0, 16.0, 21.0, 28.0, 35.0, 43.0,
49.0, 61.0, 66.0, 75.0, 89.0, 99.0], found)