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_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_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())
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_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_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 is_compatible(self, other_oriented_from, other_oriented_to,
other_overlap = None, allow_complement = True):
"""
Compares a link and optionally the complement link,
with two oriented_segments and optionally an overlap.
Parameters
----------
other_oriented_from : gfapy.OrientedLine
other_oriented_to : gfapy.OrientedLine
allow_complement : bool
Shall the complement link also be considered?
other_overlap : gfapy.Alignment.CIGAR
Compared only if not empty.
Returns
-------
bool
Does the link or, if **allow_complement**, the complement link go from
the first, oriented segment to the second with an overlap equal to the
provided one (if not empty)?
"""
other_overlap = gfapy.Alignment(other_overlap, version = "gfa1",
valid = True)
if self.is_compatible_direct(other_oriented_from, other_oriented_to,
other_overlap):
return True
elif allow_complement:
return self.is_compatible_complement(other_oriented_from,
other_oriented_to,
other_overlap)
else:
return False
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 unsafe_encode(obj):
if isinstance(obj, gfapy.Placeholder):
return str(obj)
elif isinstance(obj, list):
return ",".join([str(gfapy.Alignment(cig)) for cig in obj])
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: list, AlignmentPlaceholder)")
def validate_decoded(obj):
if isinstance(obj, gfapy.Placeholder):
pass
elif isinstance(obj, list):
for e in obj:
e = gfapy.Alignment(e, version="gfa1")
e.validate()
else:
raise gfapy.TypeError(
"the class {} is incompatible with the datatype\n".format(
obj.__class__.__name__) +
"(accepted classes: list, AlignmentPlaceholder)")
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 unsafe_decode(string):
return [ gfapy.Alignment(s, version = "gfa1", valid = True) \
for s in string.split(",") ]
def f(cig):
cig = gfapy.Alignment(cig)
cig.validate()
return str(cig)
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_string_to_placeholder(self):
self.assertIsInstance(gfapy.Alignment("*"), gfapy.Placeholder)
def decode(string):
return gfapy.Alignment(string, valid=False, version="gfa2")
def unsafe_decode(string):
return gfapy.Alignment(string, valid=True, version="gfa2")
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"))