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import unittest
import gfapy
class TestUnitAlignment(unittest.TestCase):
cigar_1 = gfapy.CIGAR([
gfapy.CIGAR.Operation(12,"M"),
gfapy.CIGAR.Operation(1,"D"),
gfapy.CIGAR.Operation(2,"I"),
gfapy.CIGAR.Operation(0,"M"),
gfapy.CIGAR.Operation(1,"P")])
cigar_1_a = [
gfapy.CIGAR.Operation(12,"M"),
gfapy.CIGAR.Operation(1,"D"),
gfapy.CIGAR.Operation(2,"I"),
gfapy.CIGAR.Operation(0,"M"),
gfapy.CIGAR.Operation(1,"P")]
cigar_1_s = "12M1D2I0M1P"
trace_1 = gfapy.Trace([12,12,0])
trace_1_s = "12,12,0"
trace_1_a = [12,12,0]
def test_list_to_alignment(self):
assert(isinstance(gfapy.Alignment([]),gfapy.AlignmentPlaceholder))
self.assertEqual(TestUnitAlignment.cigar_1, gfapy.Alignment(TestUnitAlignment.cigar_1_a))
self.assertRaises(gfapy.VersionError, gfapy.Alignment, TestUnitAlignment.trace_1_a, version="gfa1")
self.assertEqual(TestUnitAlignment.trace_1, gfapy.Alignment(TestUnitAlignment.trace_1_a, version="gfa2"))
self.assertRaises(gfapy.VersionError, gfapy.Alignment, TestUnitAlignment.cigar_1_a, version="gfaX")
self.assertRaises(gfapy.FormatError, gfapy.Alignment, ["x",2,1])
# only the first element is checked, therefore:
malformed1 = [1,2,"x"]
gfapy.Alignment(malformed1, version="gfa2") # nothing raised
assert(isinstance(gfapy.Alignment(malformed1, version="gfa2"), gfapy.Trace))
self.assertRaises(gfapy.TypeError, gfapy.Alignment(malformed1, version="gfa2").validate)
malformed2 = [gfapy.CIGAR.Operation(12,"M"),2,"x"]
gfapy.Alignment(malformed2) # nothing raised
assert(isinstance(gfapy.Alignment(malformed2),gfapy.CIGAR))
self.assertRaises(gfapy.TypeError, gfapy.Alignment(malformed2).validate)
def test_cigar_from_string(self):
self.assertEqual(TestUnitAlignment.cigar_1,
gfapy.CIGAR._from_string(TestUnitAlignment.cigar_1_s))
assert(isinstance(gfapy.CIGAR._from_string("*"),
gfapy.AlignmentPlaceholder))
self.assertEqual(TestUnitAlignment.cigar_1,
gfapy.CIGAR(TestUnitAlignment.cigar_1_a))
def test_trace_from_string(self):
self.assertEqual(TestUnitAlignment.trace_1,
gfapy.Trace._from_string(TestUnitAlignment.trace_1_s))
self.assertRaises(gfapy.FormatError, gfapy.Trace._from_string, "A,1,2")
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