def _from_list(cls, array, version = "gfa2", valid = True):
"""
Converts an alignment array into a specific list type
Parameters
----------
array : list
The alignment array.
version : str
GFA version (gfa1 or gfa2)
If *gfa1*, then CIGARs and Placeholders are supported.
If *gfa2*, also Traces are supported.
Defaults to *gfa2*.
valid : bool
If *True*, the list is guaranteed to be valid, and
further checks are skipped.
Defaults to *False*.
Returns
-------
gfapy.CIGAR or gfapy.Trace
"""
if version != "gfa1" and version != "gfa2":
raise gfapy.VersionError(
"Version error: {}".format(repr(version)))
if not array:
return gfapy.AlignmentPlaceholder()
elif isinstance(array[0], int):
if version == "gfa2":
return gfapy.Trace(array)
else:
raise gfapy.VersionError(
"Trace alignments are not allowed in GFA1: {}".format(repr(array)))
elif isinstance(array[0], gfapy.CIGAR.Operation):
return gfapy.CIGAR(array)
else:
raise gfapy.FormatError(
"Array does not represent a valid alignment field: {}"
.format(repr(array)))
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())
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")
def test_list_to_trace(self):
self.assertEqual(gfapy.Trace([12, 14, 15]),
gfapy.Alignment([12, 14, 15]))
def test_string_to_trace(self):
self.assertEqual(gfapy.Trace([12, 14, 15]),
gfapy.Alignment("12,14,15"))
def test_validation(self):
gfapy.Trace._from_string("12,12,12").validate()
self.assertRaises(gfapy.ValueError, gfapy.Trace._from_string("12,12,12").validate, ts = 10)
self.assertRaises(gfapy.ValueError, gfapy.Trace._from_string("12,-12,12").validate, ())
self.assertRaises(gfapy.TypeError, gfapy.Trace(["12x",12,12]).validate, ())
def test_from_string(self):
self.assertEqual(gfapy.Trace([12,14,15]), gfapy.Trace._from_string("12,14,15"))
with self.assertRaises(gfapy.FormatError):
gfapy.Trace._from_string("12x,12,12")
def test_str(self):
self.assertEqual("12,12,12", str(gfapy.Trace([12,12,12])))