def testDoesNotFindOutOfFrameMatches(self):
"""
Does not find matching codons that are in a non-zero frame in the
sequence.
"""
seq = Seq('TATGAAAGGGCCC')
self.assertEqual([], list(findCodons(seq, set(['ATG', 'CCC']))))
def testDoesNotFindOutOfFrameMatches(self):
"""
Does not find matching codons that are in a non-zero frame in the
sequence.
"""
seq = Seq('TATGAAAGGGCCC')
self.assertEqual([], list(findCodons(seq, set(['ATG', 'CCC']))))
def testNoMatches(self):
"""
When there are no codons in the sequence, returns an empty list.
"""
seq = Seq('AAAAAA')
self.assertEqual([], list(findCodons(seq, set(['ATG', 'AGG']))))
def testMatchMultiple(self):
"""
Finds multiple codons in the sequence.
"""
seq = Seq('ATGAAAGGGCCC')
self.assertEqual([0, 9], list(findCodons(seq, set(['ATG', 'CCC']))))
def testMatchAtEnd(self):
"""
Finds a codon at the end of the sequence.
"""
seq = Seq('ATGAAA')
self.assertEqual([3], list(findCodons(seq, set(['AAA']))))
def testMatchAtStart(self):
"""
Finds a codon at the start of the sequence.
"""
seq = Seq('ATGAAA')
self.assertEqual([0], list(findCodons(seq, set(['ATG', 'AGG']))))
def testNoMatches(self):
"""
When there are no codons in the sequence, returns an empty list.
"""
seq = Seq('AAAAAA')
self.assertEqual([], list(findCodons(seq, set(['ATG', 'AGG']))))
def testMatchMultiple(self):
"""
Finds multiple codons in the sequence.
"""
seq = Seq('ATGAAAGGGCCC')
self.assertEqual([0, 9], list(findCodons(seq, set(['ATG', 'CCC']))))
def testMatchAtEnd(self):
"""
Finds a codon at the end of the sequence.
"""
seq = Seq('ATGAAA')
self.assertEqual([3], list(findCodons(seq, set(['AAA']))))
def testMatchAtStart(self):
"""
Finds a codon at the start of the sequence.
"""
seq = Seq('ATGAAA')
self.assertEqual([0], list(findCodons(seq, set(['ATG', 'AGG']))))
