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())