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")