Python check_duplicates Examples

Example #1

File: test_align.py Project: jharman25/augur

 def test_check_duplicates_MSA_and_string_with_no_duplicates(self):
     alignment = MultipleSeqAlignment([
         SeqRecord(Seq("GTAC"), name="seq1"),
         SeqRecord(Seq("CGTT"), name="seq2"),
         SeqRecord(Seq("TAGC"), name="seq3"),
     ])
     assert align.check_duplicates(alignment, "TGTT") is None

Example #2

File: test_align.py Project: jharman25/augur

 def test_check_duplicates_MSA_and_string_with_duplicates(self):
     alignment = MultipleSeqAlignment([
         SeqRecord(Seq("GTAC"), name="seq1"),
         SeqRecord(Seq("CGTT"), name="seq2"),
         SeqRecord(Seq("TAGC"), name="seq3"),
     ])
     with pytest.raises(align.AlignmentError):
         assert align.check_duplicates(alignment, "seq3")

Example #3

 def test_check_duplicates_string_with_duplicates(self):
     with pytest.raises(align.AlignmentError):
         assert align.check_duplicates("GTAC", "CGTT", "CGTT")

Example #4

 def test_check_duplicates_strings_with_no_duplicates(self):
     assert align.check_duplicates("GTAC", "CGTT") is None

Example #5

 def test_check_duplicates_no_arguments(self):
     assert align.check_duplicates() is None