class TestFeature(unittest.TestCase):
def setUp(self):
# Set up Feature objects to be used in the tests
# Forward strand example
self.rna_data = \
Feature('CG9130-RB','chr3L','1252012','1255989','+')
# Reverse strand example
self.rna_data_2 = \
Feature('CG13051-RA','chr3L','16257914','16258166','-')
def test_properties(self):
self.assertEqual(self.rna_data.chrom,'chr3L')
self.assertEqual(self.rna_data_2.chrom,'chr3L')
def test__eq__(self):
self.assertEqual(self.rna_data,Feature('CG9130-RB',
'chr3L',
'1252012',
'1255989','+'))
self.assertNotEqual(self.rna_data,self.rna_data_2)
def test_contains_position(self):
position = 1253000
self.assertTrue(self.rna_data.containsPosition(position),
"Transcript should contain position")
position = 4250000
self.assertFalse(self.rna_data.containsPosition(position),
"Transcript should not contain position")
position = 10000
self.assertFalse(self.rna_data.containsPosition(position),
"Transcript should not contain position")
def test_get_closest_edge_distance(self):
# Single position
position = 1200000
# Single reference position
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position),
abs(self.rna_data.start-position),
"Incorrect closest edge distance #1")
position = 1300000
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position),
abs(self.rna_data.end-position),
"Incorrect closest edge distance #2")
def test_get_closest_edge_distance_outside_region(self):
# Reference region (2 positions)
position1 = 1100000
position2 = 1200000
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1,
position2),
abs(self.rna_data.start-position2),
"Incorrect closest edge distance (region #1)")
position1 = 1300000
position2 = 1400000
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1,
position2),
abs(self.rna_data.end-position1),
"Incorrect closest edge distance (region #2)")
def test_get_closest_edge_distance_partially_inside_region(self):
# Partially inside reference region
position1 = 1200000
position2 = 1255000
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1,
position2),
abs(self.rna_data.end-position2),
"Incorrect closest edge distance (inside region #1)")
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1,
position2,
zero_inside_region=True),
0,
"Incorrect closest edge distance (inside region #2)")
def test_get_closest_edge_distance_completely_inside_region(self):
# Completely inside reference region
position1 = 1250000
position2 = 1300000
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1,
position2),
abs(self.rna_data.start-position1),
"Incorrect closest edge distance (inside region #3)")
self.assertEqual(self.rna_data.getClosestEdgeDistanceTo(position1,
position2,
zero_inside_region=True),
0,
"Incorrect closest edge distance (inside region #4)")
def test_get_promoter_region(self):
leading = 10000
trailing = 2500
promoter = self.rna_data.getPromoterRegion(leading,trailing)
self.assertEqual(promoter,
(self.rna_data.getTSS()-leading,
self.rna_data.getTSS()+trailing),
"Incorrect promoter region for + strand example")
promoter = self.rna_data_2.getPromoterRegion(leading,trailing)
self.assertEqual(promoter,
(self.rna_data_2.getTSS()+leading,
self.rna_data_2.getTSS()-trailing),
"Incorrect promoter region for - strand example")
