Python findCodons Examples

Example #1

File: test_orfs.py Project: acorg/dark-matter

 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']))))

Example #2

File: test_orfs.py Project: terrycojones/dark-matter

 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']))))

Example #3

File: test_orfs.py Project: terrycojones/dark-matter

 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']))))

Example #4

File: test_orfs.py Project: terrycojones/dark-matter

 def testMatchMultiple(self):
     """
     Finds multiple codons in the sequence.
     """
     seq = Seq('ATGAAAGGGCCC')
     self.assertEqual([0, 9], list(findCodons(seq, set(['ATG', 'CCC']))))

Example #5

File: test_orfs.py Project: terrycojones/dark-matter

 def testMatchAtEnd(self):
     """
     Finds a codon at the end of the sequence.
     """
     seq = Seq('ATGAAA')
     self.assertEqual([3], list(findCodons(seq, set(['AAA']))))

Example #6

File: test_orfs.py Project: terrycojones/dark-matter

 def testMatchAtStart(self):
     """
     Finds a codon at the start of the sequence.
     """
     seq = Seq('ATGAAA')
     self.assertEqual([0], list(findCodons(seq, set(['ATG', 'AGG']))))

Example #7

File: test_orfs.py Project: acorg/dark-matter

 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']))))

Example #8

File: test_orfs.py Project: acorg/dark-matter

 def testMatchMultiple(self):
     """
     Finds multiple codons in the sequence.
     """
     seq = Seq('ATGAAAGGGCCC')
     self.assertEqual([0, 9], list(findCodons(seq, set(['ATG', 'CCC']))))

Example #9

File: test_orfs.py Project: acorg/dark-matter

 def testMatchAtEnd(self):
     """
     Finds a codon at the end of the sequence.
     """
     seq = Seq('ATGAAA')
     self.assertEqual([3], list(findCodons(seq, set(['AAA']))))

Example #10

File: test_orfs.py Project: acorg/dark-matter

 def testMatchAtStart(self):
     """
     Finds a codon at the start of the sequence.
     """
     seq = Seq('ATGAAA')
     self.assertEqual([0], list(findCodons(seq, set(['ATG', 'AGG']))))