def testPrintDescription(self):
"""
Check that the print_ method of a scanned read produces the
expected result when given a description.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
expected = ('Query: id\n'
' Length: 5\n'
' Covered indices: 5 (100.00%)\n'
' Landmark count 2, trig point count 2')
self.assertEqual(expected, read.print_(description='Query'))
def testPrintSequence(self):
"""
Check that the print_ method of a scanned read produces the
expected result when requested to print the sequence.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
expected = ('Read: id\n'
' Sequence: AAAAA\n'
' Length: 5\n'
' Covered indices: 5 (100.00%)\n'
' Landmark count 2, trig point count 2')
self.assertEqual(expected, read.print_(printSequence=True))
def testPrintFeatures(self):
"""
Check that the print_ method of a scanned read produces the
expected result when asked to print the read's features.
"""
read = ScannedRead(AARead('id', 'AAAAA'))
landmark1 = Landmark('name', 'L1', 0, 2)
landmark2 = Landmark('name', 'L2', 1, 2)
read.landmarks.extend([landmark1, landmark2])
trigPoint1 = TrigPoint('name', 'T1', 3)
trigPoint2 = TrigPoint('name', 'T2', 5)
read.trigPoints.extend([trigPoint1, trigPoint2])
expected = ('Read: id\n'
' Length: 5\n'
' Covered indices: 5 (100.00%)\n'
' Landmark count 2, trig point count 2\n'
" name symbol=L1 offset=0 len=2 detail=''\n"
" name symbol=L2 offset=1 len=2 detail=''\n"
' name symbol=T1 offset=3\n'
' name symbol=T2 offset=5')
self.assertEqual(expected, read.print_(printFeatures=True))