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import unittest
from copy import deepcopy
import gfapy
class TestApiAlignment(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_s = "12M1D2I0M1P"
cigar_gfa1_1_s = "1S2M3I4=5X6D7P8N9H"
cigar_gfa1_1_c_s = "9H8I7P6I5X4=3D2M1D"
cigar_gfa1_1_rlen = 2+4+5+6+8
cigar_gfa1_1_qlen = 1+2+3+4+5
cigar_gfa2_1_s = "1M2I3D4P"
cigar_gfa2_1_c_s = "4P3I2D1M"
cigar_gfa2_1_rlen = 1+3
cigar_gfa2_1_qlen = 1+2
trace_1 = gfapy.Trace([12,12,0])
trace_1_s = "12,12,0"
cigar_invalid_value_1 = gfapy.CIGAR([
gfapy.CIGAR.Operation(-12,"M"),
gfapy.CIGAR.Operation(1,"D"),
gfapy.CIGAR.Operation(2,"I")])
cigar_invalid_value_2 = gfapy.CIGAR([
gfapy.CIGAR.Operation(12, "Y"),
gfapy.CIGAR.Operation(1,"D"),
gfapy.CIGAR.Operation(2,"I")])
cigar_invalid_type_1 = gfapy.CIGAR([
"x",
gfapy.CIGAR.Operation(1,"D"),
gfapy.CIGAR.Operation(2,"I")])
trace_invalid_value_1 = gfapy.Trace([-2,1,12])
trace_invalid_type_1 = gfapy.Trace([12.0,1,12])
cigar_empty = gfapy.CIGAR([])
trace_empty = gfapy.Trace([])
placeholder = gfapy.AlignmentPlaceholder()
placeholder_s = "*"
string_invalid = [
"-12M1D2I", "12Y1D2I", "x1D2I",
"-2,1,12", "12.0,1,12", "*x",
]
cigar_op_1 = gfapy.CIGAR.Operation(1,"D")
cigar_op_1_s = "1D"
cigar_op_1_len = 1
cigar_op_1_code = "D"
cigar_op_2 = gfapy.CIGAR.Operation(2,"I")
cigar_op_2_s = "2I"
cigar_op_2_len = 2
cigar_op_2_code = "I"
def test_to_s(self):
self.assertEqual(TestApiAlignment.cigar_1_s, str(TestApiAlignment.cigar_1_s))
self.assertEqual(TestApiAlignment.cigar_1_s, str(TestApiAlignment.cigar_1))
self.assertEqual(TestApiAlignment.trace_1_s, str(TestApiAlignment.trace_1))
self.assertEqual(TestApiAlignment.placeholder_s, str(TestApiAlignment.placeholder))
self.assertEqual(TestApiAlignment.placeholder_s, str(TestApiAlignment.cigar_empty))
self.assertEqual(TestApiAlignment.placeholder_s, str(TestApiAlignment.trace_empty))
def test_cigar_clone(self):
cigar1_clone = deepcopy(gfapy.Alignment(TestApiAlignment.cigar_1))
self.assertEqual(TestApiAlignment.cigar_1_s, str(cigar1_clone))
cigar1_clone[0].code = "="
# copy is deep, only the clone has changed:
self.assertNotEqual(TestApiAlignment.cigar_1_s, str(cigar1_clone))
self.assertEqual(TestApiAlignment.cigar_1_s, str(TestApiAlignment.cigar_1))
def test_to_alignment(self):
self.assertEqual(TestApiAlignment.cigar_1, gfapy.Alignment(TestApiAlignment.cigar_1_s))
self.assertEqual(TestApiAlignment.trace_1, gfapy.Alignment(TestApiAlignment.trace_1_s))
self.assertEqual(TestApiAlignment.placeholder, gfapy.Alignment(TestApiAlignment.placeholder_s))
for alignment in [TestApiAlignment.cigar_1, TestApiAlignment.trace_1, TestApiAlignment.cigar_empty,
TestApiAlignment.trace_empty, TestApiAlignment.placeholder]:
self.assertEqual(alignment, gfapy.Alignment(alignment))
for string in TestApiAlignment.string_invalid:
self.assertRaises(gfapy.FormatError, gfapy.Alignment, string)
def test_decode_encode_invariant(self):
for string in [TestApiAlignment.trace_1_s, TestApiAlignment.cigar_1_s, TestApiAlignment.placeholder_s]:
self.assertEqual(string, str(gfapy.Alignment(string)))
def test_is_placeholder(self):
for a in [TestApiAlignment.cigar_empty, TestApiAlignment.trace_empty, TestApiAlignment.placeholder, TestApiAlignment.placeholder_s]:
assert(gfapy.is_placeholder(a))
for a in [TestApiAlignment.cigar_1, TestApiAlignment.cigar_1_s, TestApiAlignment.trace_1, TestApiAlignment.trace_1_s]:
assert(not gfapy.is_placeholder(a))
def test_validate(self):
TestApiAlignment.trace_1.validate() # nothing raised
TestApiAlignment.trace_empty.validate() # nothing raised
TestApiAlignment.cigar_1.validate() # nothing raised
TestApiAlignment.cigar_empty.validate() # nothing raised
TestApiAlignment.placeholder.validate() # nothing raised
self.assertRaises(gfapy.ValueError,TestApiAlignment.trace_invalid_value_1.validate)
self.assertRaises(gfapy.ValueError,TestApiAlignment.cigar_invalid_value_1.validate)
self.assertRaises(gfapy.ValueError,TestApiAlignment.cigar_invalid_value_2.validate)
self.assertRaises(gfapy.TypeError,TestApiAlignment.trace_invalid_type_1.validate)
self.assertRaises(gfapy.TypeError,TestApiAlignment.cigar_invalid_type_1.validate)
def test_version_specific_validate(self):
gfapy.Alignment(TestApiAlignment.cigar_gfa1_1_s,
version="gfa1", valid=False) # nothing raised
self.assertRaises(gfapy.FormatError, gfapy.Alignment,
TestApiAlignment.cigar_gfa1_1_s, version="gfa2", valid=False)
gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_s,
version="gfa1", valid=False) # nothing raised
gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_s,
version="gfa2", valid=False) # nothing raised
def test_array_methods(self):
for a in [TestApiAlignment.cigar_empty, TestApiAlignment.trace_empty]:
assert(not a)
for a in [TestApiAlignment.cigar_1, TestApiAlignment.trace_1]:
assert(a)
self.assertEqual(gfapy.CIGAR.Operation(1,"D"), TestApiAlignment.cigar_1[1])
self.assertEqual(12, TestApiAlignment.trace_1[1])
def test_cigar_operation_methods(self):
self.assertEqual(TestApiAlignment.cigar_op_1_len, TestApiAlignment.cigar_op_1.length)
self.assertEqual(TestApiAlignment.cigar_op_1_code, TestApiAlignment.cigar_op_1.code)
self.assertEqual(TestApiAlignment.cigar_op_1_s, str(TestApiAlignment.cigar_op_1))
TestApiAlignment.cigar_op_1.length = TestApiAlignment.cigar_op_2_len
TestApiAlignment.cigar_op_1.code = TestApiAlignment.cigar_op_2_code
self.assertEqual(TestApiAlignment.cigar_op_2, TestApiAlignment.cigar_op_1)
self.assertEqual(TestApiAlignment.cigar_op_2_len, TestApiAlignment.cigar_op_1.length)
self.assertEqual(TestApiAlignment.cigar_op_2_code, TestApiAlignment.cigar_op_1.code)
self.assertEqual(TestApiAlignment.cigar_op_2_s, str(TestApiAlignment.cigar_op_2))
def test_cigar_operation_validation(self):
TestApiAlignment.cigar_op_1.validate() # nothing raised
TestApiAlignment.cigar_op_1.validate(version="gfa2") # nothing raised
TestApiAlignment.cigar_op_2.validate() # nothing raised
TestApiAlignment.cigar_op_2.validate(version="gfa2") # nothing raised
self.assertRaises(gfapy.VersionError, TestApiAlignment.cigar_op_1.validate, version="gfaX")
stringlen = gfapy.CIGAR.Operation("1", "M")
stringlen.validate() # nothing raised
stringcode = gfapy.CIGAR.Operation(1, "M")
stringcode.validate() # nothing raised
malformed1 = gfapy.CIGAR.Operation([1], "M")
self.assertRaises(gfapy.TypeError, malformed1.validate)
malformed2 = gfapy.CIGAR.Operation(-1, "M")
self.assertRaises(gfapy.ValueError, malformed2.validate)
malformed3 = gfapy.CIGAR.Operation(1, "L")
self.assertRaises(gfapy.ValueError, malformed3.validate)
gfa1only = gfapy.CIGAR.Operation(1, "X")
gfa1only.validate() # nothing raised
self.assertRaises(gfapy.ValueError, gfa1only.validate, version="gfa2")
def test_cigar_complement(self):
self.assertEqual(TestApiAlignment.cigar_gfa1_1_c_s,
str(gfapy.Alignment(TestApiAlignment.cigar_gfa1_1_s, version="gfa1").complement()))
self.assertEqual(TestApiAlignment.cigar_gfa2_1_c_s,
str(gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_s).complement()))
def test_cigar_length_on(self):
self.assertEqual(TestApiAlignment.cigar_gfa1_1_rlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa1_1_s,version="gfa1").
length_on_reference())
self.assertEqual(TestApiAlignment.cigar_gfa1_1_qlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa1_1_s,version="gfa1").
length_on_query())
self.assertEqual(TestApiAlignment.cigar_gfa1_1_qlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa1_1_c_s,version="gfa1").
length_on_reference())
self.assertEqual(TestApiAlignment.cigar_gfa1_1_rlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa1_1_c_s,version="gfa1").
length_on_query())
self.assertEqual(TestApiAlignment.cigar_gfa2_1_rlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_s).length_on_reference())
self.assertEqual(TestApiAlignment.cigar_gfa2_1_qlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_s).length_on_query())
self.assertEqual(TestApiAlignment.cigar_gfa2_1_qlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_c_s).length_on_reference())
self.assertEqual(TestApiAlignment.cigar_gfa2_1_rlen,
gfapy.Alignment(TestApiAlignment.cigar_gfa2_1_c_s).length_on_query())
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