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import unittest
import gfapy
class TestAlignment(unittest.TestCase):
def test_string_to_cigar(self):
self.assertEqual(gfapy.CIGAR([
gfapy.CIGAR.Operation(12, "M"),
gfapy.CIGAR.Operation(1, "D"),
gfapy.CIGAR.Operation(2, "I"),
]), gfapy.Alignment("12M1D2I"))
def test_string_to_placeholder(self):
self.assertIsInstance(gfapy.Alignment("*"), gfapy.Placeholder)
def test_string_to_trace(self):
self.assertEqual(gfapy.Trace([12,14,15]),
gfapy.Alignment("12,14,15"))
def test_string_invalid(self):
self.assertRaises(gfapy.FormatError,
gfapy.Alignment, "12x1,D2I")
def test_list_to_cigar(self):
self.assertEqual(gfapy.CIGAR([
gfapy.CIGAR.Operation(12, "M"),
gfapy.CIGAR.Operation(1, "D"),
gfapy.CIGAR.Operation(2, "I")]),
gfapy.Alignment(
[gfapy.CIGAR.Operation(12, "M"),
gfapy.CIGAR.Operation(1, "D"),
gfapy.CIGAR.Operation(2, "I")]))
def test_list_to_trace(self):
self.assertEqual(gfapy.Trace([12,14,15]),
gfapy.Alignment([12,14,15]))
def test_list_invalid(self):
self.assertRaises(gfapy.FormatError,
gfapy.Alignment,["12x1", "2I"])
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