def test_exon_list(self):
exon_list = ExonList("A1BG")
self.assertEqual(exon_list.gene_symbol,"A1BG")
self.assertEqual(len(exon_list),0)
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG"))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG"))
self.assertEqual(len(exon_list),2)
def test_exon_list(self):
exon_list = ExonList("A1BG")
self.assertEqual(exon_list.gene_symbol, "A1BG")
self.assertEqual(len(exon_list), 0)
exon_list.add_exon(Exon("PSR19025918.hg.1", "A1BG"))
exon_list.add_exon(Exon("PSR19025921.hg.1", "A1BG"))
self.assertEqual(len(exon_list), 2)
def test_exon_list_iteration(self):
exon_list = ExonList("A1BG")
self.assertEqual(exon_list.gene_symbol,"A1BG")
self.assertEqual(len(exon_list),0)
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG"))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG"))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG"))
for exon,name in zip(exon_list,
("PSR19025918.hg.1",
"PSR19025921.hg.1",
"PSR19025922.hg.1")):
self.assertEqual(name,exon.name)
def test_get_best_exons_from_p_value(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1", "A1BG", p_value=0.5347865))
exon_list.add_exon(Exon("PSR19025921.hg.1", "A1BG", p_value=0.5820691))
exon_list.add_exon(Exon("PSR19025922.hg.1", "A1BG", p_value=0.7582407))
exon_list.add_exon(Exon("PSR19025925.hg.1", "A1BG", p_value=0.4111732))
exon_list.add_exon(Exon("PSR19025929.hg.1", "A1BG", p_value=0.7716908))
best_exons = exon_list.best_exons('p_value')
self.assertEqual(len(best_exons), 3)
for exon, name in zip(
best_exons,
("PSR19025925.hg.1", "PSR19025918.hg.1", "PSR19025921.hg.1")):
self.assertEqual(name, exon.name)
def test_get_best_exons_from_p_value(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",p_value=0.5347865))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",p_value=0.5820691))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",p_value=0.7582407))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",p_value=0.4111732))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",p_value=0.7716908))
best_exons = exon_list.best_exons('p_value')
self.assertEqual(len(best_exons),3)
for exon,name in zip(best_exons,("PSR19025925.hg.1",
"PSR19025918.hg.1",
"PSR19025921.hg.1")):
self.assertEqual(name,exon.name)
def test_get_best_exons_small_list(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(
Exon("PSR19025918.hg.1", "A1BG", log2_fold_change=-0.056323333))
exon_list.add_exon(
Exon("PSR19025921.hg.1", "A1BG", log2_fold_change=0.075113333))
best_exons = exon_list.best_exons('log2_fold_change')
self.assertEqual(len(best_exons), 2)
for exon, name in zip(best_exons,
("PSR19025921.hg.1", "PSR19025918.hg.1")):
self.assertEqual(name, exon.name)
def test_get_best_exons_small_list(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",log2_fold_change=-0.056323333))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",log2_fold_change=0.075113333))
best_exons = exon_list.best_exons('log2_fold_change')
self.assertEqual(len(best_exons),2)
for exon,name in zip(best_exons,("PSR19025921.hg.1",
"PSR19025918.hg.1")):
self.assertEqual(name,exon.name)
def test_exon_list_iteration(self):
exon_list = ExonList("A1BG")
self.assertEqual(exon_list.gene_symbol, "A1BG")
self.assertEqual(len(exon_list), 0)
exon_list.add_exon(Exon("PSR19025918.hg.1", "A1BG"))
exon_list.add_exon(Exon("PSR19025921.hg.1", "A1BG"))
exon_list.add_exon(Exon("PSR19025922.hg.1", "A1BG"))
for exon, name in zip(
exon_list,
("PSR19025918.hg.1", "PSR19025921.hg.1", "PSR19025922.hg.1")):
self.assertEqual(name, exon.name)
def test_average_mixed_data(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(
Exon("PSR19025918.hg.1",
"A1BG",
log2_fold_change=-0.056323333,
data=["PSR19025918.hg.1", "A1BG", 8.0, 8.5, 9.0]))
exon_list.add_exon(
Exon("PSR19025921.hg.1",
"A1BG",
log2_fold_change=0.075113333,
data=["PSR19025921.hg.1", "A1BG", 7.0, 7.0, 7.5]))
exon_list.add_exon(
Exon("PSR19025922.hg.1",
"A1BG",
log2_fold_change=0.037316667,
data=["PSR19025922.hg.1", "A1BG", 7.0, 7.5, 7.0]))
exon_list.add_exon(
Exon("PSR19025925.hg.1",
"A1BG",
log2_fold_change=-0.10211,
data=["PSR19025925.hg.1", "A1BG", 7.0, 7.5, 7.5]))
exon_list.add_exon(
Exon("PSR19025929.hg.1",
"A1BG",
log2_fold_change=-0.02433,
data=["PSR19025929.hg.1", "A1BG", 5.0, 6.0, 6.5]))
averaged_data = exon_list.average()
for average, expected in zip(averaged_data, (
None,
None,
6.8,
7.3,
7.5,
)):
self.assertEqual(average, expected)
def test_get_best_exons_from_log2_fold_change(self):
# First example
exon_list = ExonList("A1BG")
exon_list.add_exon(
Exon("PSR19025918.hg.1", "A1BG", log2_fold_change=-0.056323333))
exon_list.add_exon(
Exon("PSR19025921.hg.1", "A1BG", log2_fold_change=0.075113333))
exon_list.add_exon(
Exon("PSR19025922.hg.1", "A1BG", log2_fold_change=0.037316667))
exon_list.add_exon(
Exon("PSR19025925.hg.1", "A1BG", log2_fold_change=-0.10211))
exon_list.add_exon(
Exon("PSR19025929.hg.1", "A1BG", log2_fold_change=-0.02433))
best_exons = exon_list.best_exons('log2_fold_change')
self.assertEqual(len(best_exons), 3)
for exon, name in zip(
best_exons,
("PSR19025925.hg.1", "PSR19025918.hg.1", "PSR19025929.hg.1")):
self.assertEqual(name, exon.name)
# Second example
exon_list = ExonList("A1BG")
exon_list.add_exon(
Exon("PSR19025926.hg.1", "A1BG", log2_fold_change=0.059556667))
exon_list.add_exon(
Exon("PSR19025927.hg.1", "A1BG", log2_fold_change=0.119746667))
exon_list.add_exon(
Exon("PSR19025928.hg.1", "A1BG", log2_fold_change=-0.090296667))
exon_list.add_exon(
Exon("PSR19025929.hg.1", "A1BG", log2_fold_change=-0.02433))
exon_list.add_exon(
Exon("PSR19025930.hg.1", "A1BG", log2_fold_change=0.02569))
best_exons = exon_list.best_exons('log2_fold_change')
self.assertEqual(len(best_exons), 3)
for exon, name in zip(
best_exons,
("PSR19025927.hg.1", "PSR19025926.hg.1", "PSR19025930.hg.1")):
self.assertEqual(name, exon.name)
def test_get_best_exon_from_log2_fold_change(self):
# First example
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",log2_fold_change=-0.056323333))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",log2_fold_change=0.075113333))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",log2_fold_change=0.037316667))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",log2_fold_change=-0.10211))
exon_list.add_exon(Exon("PSR19025926.hg.1","A1BG",log2_fold_change=0.059556667))
exon_list.add_exon(Exon("PSR19025927.hg.1","A1BG",log2_fold_change=0.119746667))
exon_list.add_exon(Exon("PSR19025928.hg.1","A1BG",log2_fold_change=-0.090296667))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",log2_fold_change=-0.02433))
exon_list.add_exon(Exon("PSR19025930.hg.1","A1BG",log2_fold_change=0.02569))
best_exon = exon_list.best_exon('log2_fold_change')
self.assertEqual(best_exon.name,"PSR19025927.hg.1")
# Second example
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",log2_fold_change=-0.056323333))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",log2_fold_change=0.075113333))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",log2_fold_change=0.037316667))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",log2_fold_change=-0.10211))
exon_list.add_exon(Exon("PSR19025926.hg.1","A1BG",log2_fold_change=0.059556667))
exon_list.add_exon(Exon("PSR19025928.hg.1","A1BG",log2_fold_change=-0.090296667))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",log2_fold_change=-0.02433))
exon_list.add_exon(Exon("PSR19025930.hg.1","A1BG",log2_fold_change=0.02569))
best_exon = exon_list.best_exon('log2_fold_change')
self.assertEqual(best_exon.name,"PSR19025925.hg.1")
def test_exon_list_sort_on_p_value(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",p_value=0.5347865))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",p_value=0.5820691))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",p_value=0.7582407))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",p_value=0.4111732))
exon_list.add_exon(Exon("PSR19025926.hg.1","A1BG",p_value=0.6550312))
exon_list.add_exon(Exon("PSR19025927.hg.1","A1BG",p_value=0.5002532))
exon_list.add_exon(Exon("PSR19025928.hg.1","A1BG",p_value=0.3521274))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",p_value=0.7716908))
exon_list.add_exon(Exon("PSR19025930.hg.1","A1BG",p_value=0.7720515))
exon_list.sort('p_value')
last_p_value = None
for exon in exon_list.exons:
if last_p_value is not None:
self.assertTrue(last_p_value <= exon.p_value)
last_p_value = exon.p_value
def test_exon_list_sort_on_log2_fold_change(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",log2_fold_change=-0.056323333))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",log2_fold_change=0.075113333))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",log2_fold_change=0.037316667))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",log2_fold_change=-0.10211))
exon_list.add_exon(Exon("PSR19025926.hg.1","A1BG",log2_fold_change=0.059556667))
exon_list.add_exon(Exon("PSR19025927.hg.1","A1BG",log2_fold_change=0.119746667))
exon_list.add_exon(Exon("PSR19025928.hg.1","A1BG",log2_fold_change=-0.090296667))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",log2_fold_change=-0.02433))
exon_list.add_exon(Exon("PSR19025930.hg.1","A1BG",log2_fold_change=0.02569))
exon_list.sort('log2_fold_change')
last_log2_fold_change = None
for exon in exon_list.exons:
if last_log2_fold_change is not None:
self.assertTrue(last_log2_fold_change >= exon.log2_fold_change)
last_log2_fold_change = exon.log2_fold_change
def test_average_mixed_data(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",log2_fold_change=-0.056323333,
data=["PSR19025918.hg.1","A1BG",8.0,8.5,9.0]))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",log2_fold_change=0.075113333,
data=["PSR19025921.hg.1","A1BG",7.0,7.0,7.5]))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",log2_fold_change=0.037316667,
data=["PSR19025922.hg.1","A1BG",7.0,7.5,7.0]))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",log2_fold_change=-0.10211,
data=["PSR19025925.hg.1","A1BG",7.0,7.5,7.5]))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",log2_fold_change=-0.02433,
data=["PSR19025929.hg.1","A1BG",5.0,6.0,6.5]))
averaged_data = exon_list.average()
for average,expected in zip(averaged_data,(None,
None,
6.8,
7.3,
7.5,)):
self.assertEqual(average,expected)
def test_exon_list_sort_on_log2_fold_change(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(
Exon("PSR19025918.hg.1", "A1BG", log2_fold_change=-0.056323333))
exon_list.add_exon(
Exon("PSR19025921.hg.1", "A1BG", log2_fold_change=0.075113333))
exon_list.add_exon(
Exon("PSR19025922.hg.1", "A1BG", log2_fold_change=0.037316667))
exon_list.add_exon(
Exon("PSR19025925.hg.1", "A1BG", log2_fold_change=-0.10211))
exon_list.add_exon(
Exon("PSR19025926.hg.1", "A1BG", log2_fold_change=0.059556667))
exon_list.add_exon(
Exon("PSR19025927.hg.1", "A1BG", log2_fold_change=0.119746667))
exon_list.add_exon(
Exon("PSR19025928.hg.1", "A1BG", log2_fold_change=-0.090296667))
exon_list.add_exon(
Exon("PSR19025929.hg.1", "A1BG", log2_fold_change=-0.02433))
exon_list.add_exon(
Exon("PSR19025930.hg.1", "A1BG", log2_fold_change=0.02569))
exon_list.sort('log2_fold_change')
last_log2_fold_change = None
for exon in exon_list.exons:
if last_log2_fold_change is not None:
self.assertTrue(last_log2_fold_change >= exon.log2_fold_change)
last_log2_fold_change = exon.log2_fold_change
def test_get_best_exon_from_p_value(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1", "A1BG", p_value=0.5347865))
exon_list.add_exon(Exon("PSR19025921.hg.1", "A1BG", p_value=0.5820691))
exon_list.add_exon(Exon("PSR19025922.hg.1", "A1BG", p_value=0.7582407))
exon_list.add_exon(Exon("PSR19025925.hg.1", "A1BG", p_value=0.4111732))
exon_list.add_exon(Exon("PSR19025926.hg.1", "A1BG", p_value=0.6550312))
exon_list.add_exon(Exon("PSR19025927.hg.1", "A1BG", p_value=0.5002532))
exon_list.add_exon(Exon("PSR19025928.hg.1", "A1BG", p_value=0.3521274))
exon_list.add_exon(Exon("PSR19025929.hg.1", "A1BG", p_value=0.7716908))
exon_list.add_exon(Exon("PSR19025930.hg.1", "A1BG", p_value=0.7720515))
best_exon = exon_list.best_exon('p_value')
self.assertEqual(best_exon.name, "PSR19025928.hg.1")
def test_exon_list_sort_on_p_value(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1", "A1BG", p_value=0.5347865))
exon_list.add_exon(Exon("PSR19025921.hg.1", "A1BG", p_value=0.5820691))
exon_list.add_exon(Exon("PSR19025922.hg.1", "A1BG", p_value=0.7582407))
exon_list.add_exon(Exon("PSR19025925.hg.1", "A1BG", p_value=0.4111732))
exon_list.add_exon(Exon("PSR19025926.hg.1", "A1BG", p_value=0.6550312))
exon_list.add_exon(Exon("PSR19025927.hg.1", "A1BG", p_value=0.5002532))
exon_list.add_exon(Exon("PSR19025928.hg.1", "A1BG", p_value=0.3521274))
exon_list.add_exon(Exon("PSR19025929.hg.1", "A1BG", p_value=0.7716908))
exon_list.add_exon(Exon("PSR19025930.hg.1", "A1BG", p_value=0.7720515))
exon_list.sort('p_value')
last_p_value = None
for exon in exon_list.exons:
if last_p_value is not None:
self.assertTrue(last_p_value <= exon.p_value)
last_p_value = exon.p_value
def test_get_best_exon_from_p_value(self):
exon_list = ExonList("A1BG")
exon_list.add_exon(Exon("PSR19025918.hg.1","A1BG",p_value=0.5347865))
exon_list.add_exon(Exon("PSR19025921.hg.1","A1BG",p_value=0.5820691))
exon_list.add_exon(Exon("PSR19025922.hg.1","A1BG",p_value=0.7582407))
exon_list.add_exon(Exon("PSR19025925.hg.1","A1BG",p_value=0.4111732))
exon_list.add_exon(Exon("PSR19025926.hg.1","A1BG",p_value=0.6550312))
exon_list.add_exon(Exon("PSR19025927.hg.1","A1BG",p_value=0.5002532))
exon_list.add_exon(Exon("PSR19025928.hg.1","A1BG",p_value=0.3521274))
exon_list.add_exon(Exon("PSR19025929.hg.1","A1BG",p_value=0.7716908))
exon_list.add_exon(Exon("PSR19025930.hg.1","A1BG",p_value=0.7720515))
best_exon = exon_list.best_exon('p_value')
self.assertEqual(best_exon.name,"PSR19025928.hg.1")
