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_no_data(self):
exon = Exon("PSR19025918.hg.1", "A1BG")
self.assertEqual(exon.name, "PSR19025918.hg.1")
self.assertEqual(exon.gene_symbol, "A1BG")
self.assertEqual(exon.log2_fold_change, None)
self.assertEqual(exon.p_value, None)
self.assertEqual(
str(exon),
"PSR19025918.hg.1:A1BG:log2FoldChange=None;p-value=None")
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_with_data(self):
log2_fold_change = -0.056323333
p_value = 0.5347865
exon = Exon("PSR19025918.hg.1",
"A1BG",
log2_fold_change=log2_fold_change,
p_value=p_value)
self.assertEqual(exon.name, "PSR19025918.hg.1")
self.assertEqual(exon.gene_symbol, "A1BG")
self.assertEqual(exon.log2_fold_change, log2_fold_change)
self.assertEqual(exon.p_value, p_value)
self.assertEqual(
str(exon), "PSR19025918.hg.1:A1BG:log2FoldChange=%s;p-value=%s" %
(float(log2_fold_change), float(p_value)))
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_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)