def test_require_parents_equal_except_location(self):
with pytest.raises(MismatchedParentException):
ObjectValidation.require_parents_equal_except_location(
Parent(id="parent1"), Parent(id="parent2"))
ObjectValidation.require_parents_equal_except_location(
Parent(id="parent", location=SingleInterval(0, 5, Strand.PLUS)),
Parent(id="parent", location=SingleInterval(10, 20, Strand.MINUS)),
)
def test_init(self):
sequence = Sequence(
"ACTG",
Alphabet.NT_STRICT,
id="id",
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
location=SingleInterval(5, 9, Strand.MINUS, parent="parent"),
),
)
# Sequence data
assert sequence.sequence == Seq("ACTG")
assert str(sequence) == "ACTG"
# Alphabet
assert sequence.alphabet == Alphabet.NT_STRICT
# ID
assert sequence.id == "id"
# Sequence type
assert sequence.sequence_type == "seqtype_1"
# Parent ID
assert sequence.parent_id == "parent"
assert Sequence("A", Alphabet.NT_STRICT,
parent="parent").parent_id == "parent"
assert (Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(
location=SingleInterval(5, 6, Strand.MINUS, parent="parent")),
).parent_id == "parent")
assert Sequence("A", Alphabet.NT_STRICT).parent_id is None
# Parent type
assert sequence.parent_type == "seqtype_2"
# Parent strand
assert sequence.parent_strand == Strand.MINUS
assert Sequence(
"A", Alphabet.NT_STRICT,
parent=Strand.UNSTRANDED).parent_strand == Strand.UNSTRANDED
# Location on parent
assert (Sequence(
"A",
Alphabet.NT_STRICT,
parent=SingleInterval(3, 4, Strand.UNSTRANDED),
).parent_strand == Strand.UNSTRANDED)
assert Sequence("A", Alphabet.NT_STRICT).parent_strand is None
assert sequence.location_on_parent == SingleInterval(5,
9,
Strand.MINUS,
parent="parent")
# No alphabet validation
Sequence("xxx", Alphabet.NT_STRICT, validate_alphabet=False)
def test_require_parent_has_parent_with_location(self):
with pytest.raises(NullParentException):
ObjectValidation.require_parent_has_parent_with_location(
Parent(id="parent"))
with pytest.raises(NullParentException):
ObjectValidation.require_parent_has_parent_with_location(
Parent(id="parent", parent="grandparent"))
ObjectValidation.require_parent_has_parent_with_location(
Parent(
id="parent",
parent=Parent(id="grandparent",
location=SingleInterval(0, 5, Strand.PLUS)),
))
def liftover_to_parent_or_seq_chunk_parent(
self,
parent_or_seq_chunk_parent: Parent,
) -> "AbstractInterval":
"""
This function returns a copy of this interval lifted over to a new coordinate system. If this interval
is already in chunk-relative coordinates, it is first lifted back up the chromosome coordinates before
the liftover occurs. This means that there *must* be a Parent somewhere in the ancestry with
type "chromosome", and that Parent must match the supplied parent except for location information.
Validation has to happen here in addition to in ``liftover_location_to_seq_chunk_parent()``, because
at this point the parent of this current interval is still known. Once the ``to_dict()`` operation is performed,
this information is list, and the new parent is applied under the assumption that it is valid.
"""
if self.chunk_relative_location.has_ancestor_of_type(SequenceType.SEQUENCE_CHUNK):
if not self.chunk_relative_location.has_ancestor_of_type(SequenceType.CHROMOSOME):
raise NoSuchAncestorException(
"This location does not have a chromosome ancestor of its sequence chunk, "
"which means it is not possible to lift to a new a chunk through the chromosome coordinates."
)
if self.chunk_relative_location.has_ancestor_of_type(SequenceType.CHROMOSOME):
loc_chrom = self.chunk_relative_location.first_ancestor_of_type(SequenceType.CHROMOSOME)
par_chrom = parent_or_seq_chunk_parent.first_ancestor_of_type(SequenceType.CHROMOSOME)
if loc_chrom.sequence and par_chrom.sequence:
ObjectValidation.require_parents_equal_except_location(loc_chrom, par_chrom)
else:
ObjectValidation.require_parents_equal_except_location_and_sequence(loc_chrom, par_chrom)
return self.from_dict(self.to_dict(), parent_or_seq_chunk_parent)
def test_init(self, id, sequence_type, strand, location, sequence, expected):
assert expected == Parent(
id=id,
sequence_type=sequence_type,
strand=strand,
location=location,
sequence=sequence,
)
def test_seq_chunk_to_parent(strand):
obs = seq_chunk_to_parent("ATGCATGC", "TestSeq", 200, 208, strand=strand)
assert obs == Parent(
id="TestSeq:200-208",
sequence_type=SequenceType.SEQUENCE_CHUNK,
strand=None,
location=None,
sequence=Sequence(
data="ATGCATGC",
id="TestSeq:200-208",
alphabet=Alphabet.NT_EXTENDED_GAPPED,
type=SequenceType.SEQUENCE_CHUNK,
parent=Parent(
id="TestSeq",
sequence_type=SequenceType.CHROMOSOME,
strand=strand,
location=SingleInterval(
200,
208,
strand,
parent=Parent(
id="TestSeq",
sequence_type=SequenceType.CHROMOSOME,
strand=strand,
location=SingleInterval(200, 208, strand),
sequence=None,
parent=None,
),
),
sequence=None,
parent=Parent(
id="TestSeq",
sequence_type=SequenceType.CHROMOSOME,
strand=strand,
location=SingleInterval(200, 208, strand, parent=None),
sequence=None,
parent=None,
),
),
),
)
assert obs.has_ancestor_of_type(SequenceType.CHROMOSOME)
assert obs.has_ancestor_of_type(SequenceType.SEQUENCE_CHUNK)
def test_init_error(self, id, sequence_type, strand, location, sequence, parent, expected_exception):
with pytest.raises(expected_exception):
Parent(
id=id,
sequence_type=sequence_type,
strand=strand,
location=location,
sequence=sequence,
parent=parent,
)
def seq_chunk_to_parent(
seq: str,
sequence_name: Union[UUID, str],
start: int,
end: int,
strand: Optional[Strand] = Strand.PLUS,
alphabet: Optional[Alphabet] = Alphabet.NT_EXTENDED_GAPPED,
) -> Parent:
"""Construct a sequence chunk parent from a sequence. This is used when an annotation collection is being
instantiated with a subset of a genome sequence.
NOTE: This sequence is assumed to be a subset of a chromosome. There is no way to validate that within this
function.
Args:
seq: Sequence subset to use.
sequence_name: The name of the sequence.
start: The genomic start position of this sequence.
end: The genomic end position of this sequence.
strand: The strand this chunk is relative to the genome.
alphabet: The alphabet the sequence is in.
Returns:
An instantiated Parent object ready to be passed to a constructor.
"""
chunk_id = f"{sequence_name}:{start}-{end}"
return Parent(
id=chunk_id,
sequence=Sequence(
seq,
alphabet,
id=chunk_id,
type=SequenceType.SEQUENCE_CHUNK,
parent=Parent(location=SingleInterval(
start,
end,
strand,
parent=Parent(id=sequence_name,
sequence_type=SequenceType.CHROMOSOME),
)),
),
)
def test_seq_to_parent():
seq = "ATGCATGC"
seq_id = "TestSeq"
obs = seq_to_parent(seq, seq_id=seq_id)
assert obs == Parent(
sequence=Sequence(seq,
Alphabet.NT_EXTENDED_GAPPED,
type=SequenceType.CHROMOSOME,
id=seq_id),
location=SingleInterval(0, len(seq), Strand.PLUS),
)
def test_require_location_has_parent_with_sequence(self):
with pytest.raises(NullParentException):
ObjectValidation.require_location_has_parent_with_sequence(
SingleInterval(0, 5, Strand.PLUS))
with pytest.raises(NullSequenceException):
ObjectValidation.require_location_has_parent_with_sequence(
SingleInterval(0, 5, Strand.PLUS, parent="parent"))
ObjectValidation.require_location_has_parent_with_sequence(
SingleInterval(
0,
5,
Strand.PLUS,
parent=Parent(id="parent",
sequence=Sequence("AAAAA", Alphabet.NT_STRICT)),
))
def first_ancestor_of_type(self,
sequence_type: str,
include_self: bool = True) -> Parent:
"""Returns the Parent object representing the closest ancestor (parent, parent of parent, etc.)
of this sequence which has the given sequence type. If include_self is True and this sequence has the
given type, returns a new Parent object representing this sequence. Raises NoSuchAncestorException
if no ancestor with the given type exists.
Parameters
----------
sequence_type:
Sequence type
include_self:
Include this sequence as a candidate
"""
if include_self and self.sequence_type == sequence_type:
return Parent(sequence=self)
if self.parent:
return self.parent.first_ancestor_of_type(sequence_type, True)
raise NoSuchAncestorException
def test_init_invalid_params(
self,
data,
alphabet,
parent_id,
parent_type,
parent_strand,
location_on_parent,
expected_exception,
):
with pytest.raises(expected_exception):
Sequence(
data,
alphabet,
parent=Parent(
id=parent_id,
sequence_type=parent_type,
strand=parent_strand,
location=location_on_parent,
),
)
def seq_to_parent(
seq: str,
alphabet: Optional[Alphabet] = Alphabet.NT_EXTENDED_GAPPED,
seq_id: Optional[str] = None,
seq_type: Optional[str] = SequenceType.CHROMOSOME,
) -> Parent:
"""Convert a string into a Parent object. This is the intermediate that transfers a BioPython sequence object to
a BioCantor sequence object.
NOTE: This sequence is assumed to be the entire chromosome.
Args:
seq: String of sequence.
alphabet: Alphabet this sequence is in.
seq_id: ID to attach to the Parent.
seq_type: Sequence type to attach to the Parent.
Returns:
A :class:`Parent` object.
"""
return Parent(sequence=Sequence(seq, alphabet, type=seq_type, id=seq_id),
location=SingleInterval(0, len(seq), Strand.PLUS))
def reverse_complement(self,
new_id: str = None,
new_type: str = None) -> "Sequence":
"""Returns a new Sequence corresponding to the reverse complement of this Sequence.
Location on parent, if it exists, is converted appropriately.
Parameters
----------
new_id
ID for the returned Sequence. If no value is provided, None is used.
new_type
Sequence type for the returned Sequence. If no value is provided, None is used.
"""
if not self.alphabet.is_nucleotide_alphabet():
raise AlphabetError(
"Cannot reverse complement sequence with alphabet {}".format(
self.alphabet))
location = self.location_on_parent.reverse_strand(
) if self.location_on_parent else None
strand = self.parent_strand.reverse() if self.parent_strand else None
rc_map = ALPHABET_TO_NUCLEOTIDE_COMPLEMENT[self.alphabet]
try:
seq_data = "".join((rc_map[c] for c in reversed(str(self))))
except KeyError as e:
raise AlphabetError(
"Character {} not found for alphabet {}".format(
str(e), self.alphabet))
rc_parent = Parent(strand=strand,
location=location) if strand or location else None
return Sequence(
seq_data,
self.alphabet,
id=new_id,
type=new_type,
parent=rc_parent,
validate_alphabet=False,
)
def test_require_parent_has_location(self):
with pytest.raises(NullParentException):
ObjectValidation.require_parent_has_location(Parent(id="parent"))
ObjectValidation.require_parent_has_location(
Parent(location=SingleInterval(5, 6, Strand.PLUS)))
def _(obj) -> Parent:
return Parent(strand=obj)
def _(obj) -> Parent:
return Parent(location=obj)
class TestParent:
@pytest.mark.parametrize(
"id,sequence_type,strand,location,sequence,expected",
[
(None, None, None, None, None, Parent()),
(
"id",
"seqtype",
Strand.MINUS,
SingleInterval(
0,
1,
Strand.MINUS,
Parent(
id="id",
sequence_type="seqtype",
strand=Strand.MINUS,
sequence=Sequence(
"AAA",
Alphabet.NT_STRICT,
id="id",
type="seqtype",
parent=Parent(
id="id2",
sequence=Sequence("CCC", Alphabet.NT_STRICT, id="id2"),
),
),
),
),
Sequence(
"AAA",
Alphabet.NT_STRICT,
id="id",
type="seqtype",
parent=Parent(id="id2", sequence=Sequence("CCC", Alphabet.NT_STRICT, id="id2")),
),
Parent(
id="id",
sequence_type="seqtype",
strand=Strand.MINUS,
location=SingleInterval(
0,
1,
Strand.MINUS,
Parent(
id="id",
sequence_type="seqtype",
strand=Strand.MINUS,
sequence=Sequence(
"AAA",
Alphabet.NT_STRICT,
id="id",
type="seqtype",
parent=Parent(
id="id2",
sequence=Sequence("CCC", Alphabet.NT_STRICT, id="id2"),
),
),
),
),
sequence=Sequence(
"AAA",
Alphabet.NT_STRICT,
id="id",
type="seqtype",
parent=Parent(
id="id2",
sequence=Sequence("CCC", Alphabet.NT_STRICT, id="id2"),
),
),
),
),
],
)
def test_init(self, id, sequence_type, strand, location, sequence, expected):
assert expected == Parent(
id=id,
sequence_type=sequence_type,
strand=strand,
location=location,
sequence=sequence,
)
@pytest.mark.parametrize(
"id,sequence_type,strand,location,sequence,parent,expected_exception",
[
("id1", None, None, SingleInterval(0, 5, Strand.PLUS, parent="id2"), None, None, ParentException),
("id1", None, None, None, Sequence("AAA", Alphabet.NT_STRICT, id="id2"), None, ParentException),
(
None,
None,
None,
SingleInterval(0, 5, Strand.PLUS, parent="id1"),
Sequence("AAC", Alphabet.NT_STRICT, id="id2"),
None,
ParentException,
),
(
None,
"seqtype",
None,
SingleInterval(0, 5, Strand.PLUS, parent=Parent(sequence_type="unknown")),
None,
None,
ParentException,
),
(None, "seqtype", None, None, Sequence("AAT", Alphabet.NT_STRICT, type="unknown"), None, ParentException),
(
None,
None,
None,
SingleInterval(0, 5, Strand.PLUS, parent=Parent(sequence_type="unknown")),
Sequence("AAG", Alphabet.NT_STRICT, type="seqtype"),
None,
ParentException,
),
(None, None, Strand.MINUS, SingleInterval(0, 5, Strand.PLUS), None, None, InvalidStrandException),
(
None,
None,
None,
SingleInterval(0, 10, Strand.PLUS),
Sequence("A", Alphabet.NT_STRICT),
None,
InvalidPositionException,
),
(
None,
None,
None,
None,
Sequence("AA", Alphabet.NT_STRICT),
Parent(sequence=Sequence("A", Alphabet.NT_STRICT)),
LocationException,
),
(None, None, Strand.PLUS, SingleInterval(5, 10, Strand.MINUS), None, None, InvalidStrandException),
(
None,
None,
None,
None,
Sequence("AA", Alphabet.NT_STRICT, parent="id1"),
Parent(id="id2"),
MismatchedParentException,
),
],
)
def test_init_error(self, id, sequence_type, strand, location, sequence, parent, expected_exception):
with pytest.raises(expected_exception):
Parent(
id=id,
sequence_type=sequence_type,
strand=strand,
location=location,
sequence=sequence,
parent=parent,
)
@pytest.mark.parametrize(
"obj,expected",
[
(
Sequence("AAA", Alphabet.NT_STRICT),
Parent(sequence=Sequence("AAA", Alphabet.NT_STRICT)),
),
("parent", Parent(id="parent")),
(
SingleInterval(5, 10, Strand.PLUS),
Parent(location=SingleInterval(5, 10, Strand.PLUS)),
),
(
CompoundInterval([5], [10], Strand.PLUS),
Parent(location=CompoundInterval([5], [10], Strand.PLUS)),
),
(EmptyLocation(), Parent(location=EmptyLocation())),
(Strand.MINUS, Parent(strand=Strand.MINUS)),
(
Parent(
id="parent",
sequence_type="chr",
strand=Strand.MINUS,
parent=Parent(id="grandparent"),
),
Parent(
id="parent",
sequence_type="chr",
strand=Strand.MINUS,
parent=Parent(id="grandparent"),
),
),
],
)
def test_make_parent(self, obj, expected):
assert make_parent(obj) == expected
@pytest.mark.parametrize(
"parent1,parent2,expected",
[
(Parent(), Parent(), True),
(Parent(), Parent(id=None, sequence_type=None), True),
(Parent(id="id1"), Parent(id="id2"), False),
(
Parent(sequence_type=None),
Parent(sequence_type="unknown"),
False,
),
(Parent(strand=Strand.UNSTRANDED), Parent(strand=Strand.MINUS), False),
(
Parent(location=SingleInterval(0, 5, Strand.PLUS, parent="id1")),
Parent(location=SingleInterval(0, 5, Strand.PLUS, parent="id2")),
False,
),
(
Parent(sequence=Sequence("A", Alphabet.NT_STRICT)),
Parent(sequence=Sequence("A", Alphabet.NT_STRICT, parent=Parent(id="parent"))),
False,
),
(
Parent(parent="parent1"),
Parent(parent="parent2"),
False,
),
],
)
def test_eq(self, parent1, parent2, expected):
assert (parent1 == parent2) is expected
@pytest.mark.parametrize(
"parent1,parent2,expected",
[
(Parent(), Parent(), True),
(Parent(id="id1"), Parent(id="id2"), False),
(
Parent(sequence_type=None),
Parent(sequence_type="unknown"),
False,
),
(Parent(strand=Strand.UNSTRANDED), Parent(strand=Strand.MINUS), True),
(
Parent(location=SingleInterval(0, 5, Strand.PLUS, parent="id1")),
Parent(location=SingleInterval(0, 5, Strand.PLUS, parent="id2")),
False,
),
(
Parent(sequence=Sequence("A", Alphabet.NT_STRICT)),
Parent(sequence=Sequence("A", Alphabet.NT_STRICT, parent="parent")),
False,
),
(
Parent(parent="parent1"),
Parent(parent="parent2"),
False,
),
],
)
def test_equals_except_location(self, parent1, parent2, expected):
assert parent1.equals_except_location(parent2) is expected
@pytest.mark.parametrize(
"id,location,sequence,expected",
[
("id", None, None, "id"),
(
None,
SingleInterval(0, 1, Strand.PLUS, parent="id"),
None,
"id",
),
(
None,
None,
Sequence("A", Alphabet.NT_STRICT, id="id", parent="id2"),
"id",
),
(
"id",
SingleInterval(0, 1, Strand.PLUS, parent="id"),
Sequence("A", Alphabet.NT_STRICT, id="id", parent="id2"),
"id",
),
],
)
def test_id(self, id, location, sequence, expected):
assert Parent(id=id, location=location, sequence=sequence).id == expected
@pytest.mark.parametrize(
"sequence_type,location,sequence,expected",
[
("seqtype", None, None, "seqtype"),
(
None,
SingleInterval(
0,
5,
Strand.PLUS,
parent=Parent(sequence_type="seqtype"),
),
None,
"seqtype",
),
(
None,
None,
Sequence("A", Alphabet.NT_STRICT, type="seqtype"),
"seqtype",
),
(
None,
None,
Sequence(
"A",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(sequence_type="seqtype_2"),
),
"seqtype",
),
],
)
def test_sequence_type(self, sequence_type, location, sequence, expected):
assert Parent(sequence_type=sequence_type, location=location, sequence=sequence).sequence_type == expected
@pytest.mark.parametrize(
"strand,location,sequence,expected",
[
(Strand.PLUS, None, None, Strand.PLUS),
(None, SingleInterval(0, 5, Strand.MINUS), None, Strand.MINUS),
(
Strand.PLUS,
None,
Sequence("A", Alphabet.NT_STRICT, parent=Strand.MINUS),
Strand.PLUS,
),
],
)
def test_strand(self, strand, location, sequence, expected):
assert Parent(strand=strand, location=location, sequence=sequence).strand == expected
def test_location(self):
assert Parent(location=SingleInterval(0, 1, Strand.PLUS)).location == SingleInterval(0, 1, Strand.PLUS)
def test_sequence(self):
assert Parent(sequence=Sequence("A", Alphabet.NT_STRICT)).sequence == Sequence("A", Alphabet.NT_STRICT)
@pytest.mark.parametrize(
"parent,expected",
[
(Parent(parent="id"), Parent(id="id")),
(
Parent(
sequence=Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(sequence_type="chr"),
)
),
Parent(sequence_type="chr"),
),
],
)
def test_parent(self, parent, expected):
assert parent.parent == expected
@pytest.mark.parametrize(
"parent,expected",
[
(Parent(), Parent()),
(Parent(strand=Strand.PLUS), Parent()),
(
Parent(strand=Strand.PLUS, location=SingleInterval(5, 10, Strand.PLUS)),
Parent(),
),
(
Parent(
id="parent",
sequence_type="unknown",
strand=Strand.PLUS,
location=SingleInterval(0, 1, Strand.PLUS),
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
Parent(
id="parent",
sequence_type="unknown",
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
],
)
def test_strip_location_info(self, parent, expected):
assert parent.strip_location_info() == expected
@pytest.mark.parametrize(
"parent,sequence_type,include_self,expected",
[
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
True,
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
),
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
False,
Parent(id="parent", sequence_type="seqtype"),
),
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent", sequence_type="seqtype_2"),
),
),
"seqtype_2",
True,
Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent", sequence_type="seqtype_2"),
),
),
],
)
def test_first_ancestor_of_type(self, parent, sequence_type, include_self, expected):
assert parent.first_ancestor_of_type(sequence_type, include_self=include_self) == expected
@pytest.mark.parametrize(
"parent,sequence_type,include_self",
[
(Parent(id="self"), "seqtype_2", True),
(
Parent(id="self", parent="parent"),
"seqtype_2",
True,
),
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent", sequence_type="seqtype_2"),
),
),
"chr",
True,
),
],
)
def test_first_ancestor_of_type_error(self, parent, sequence_type, include_self):
with pytest.raises(NoSuchAncestorException):
parent.first_ancestor_of_type(sequence_type, include_self=include_self)
@pytest.mark.parametrize(
"parent,sequence_type,include_self,expected",
[
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
True,
True,
),
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
False,
True,
),
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent", sequence_type="seqtype_2"),
),
),
"seqtype_2",
True,
True,
),
(
Parent(id="self"),
"seqtype_2",
True,
False,
),
(
Parent(id="self", parent="parent"),
"seqtype_2",
True,
False,
),
(
Parent(
id="self",
sequence_type="seqtype",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent", sequence_type="seqtype_2"),
),
),
"chr",
True,
False,
),
],
)
def test_has_ancestor_of_type(self, parent, sequence_type, include_self, expected):
assert parent.has_ancestor_of_type(sequence_type, include_self=include_self) is expected
@pytest.mark.parametrize(
"parent,expected",
[
(
Parent(
id="parent",
location=SingleInterval(3, 5, Strand.PLUS),
parent=Parent(id="grandparent", location=SingleInterval(10, 20, Strand.PLUS)),
),
SingleInterval(13, 15, Strand.PLUS, parent="grandparent"),
),
(
Parent(
id="parent",
location=SingleInterval(0, 5, Strand.PLUS),
sequence_type="unknown",
strand=Strand.PLUS,
parent=Parent(
id="grandparent",
location=SingleInterval(100, 200, Strand.MINUS),
),
),
SingleInterval(195, 200, Strand.MINUS, parent="grandparent"),
),
(
Parent(
id="parent",
location=SingleInterval(6, 9, Strand.MINUS),
parent=Parent(
id="grandparent",
location=SingleInterval(0, 10, Strand.PLUS),
sequence_type="chr",
strand=Strand.PLUS,
parent="great grandparent",
),
),
SingleInterval(
6,
9,
Strand.MINUS,
parent=Parent(
id="grandparent",
sequence_type="chr",
parent="great grandparent",
),
),
),
(
Parent(
id="parent",
sequence_type="chr",
strand=Strand.MINUS,
location=SingleInterval(6, 8, Strand.MINUS),
parent=Parent(
id="grandparent",
sequence_type="unknown",
strand=Strand.MINUS,
location=SingleInterval(5, 15, Strand.MINUS),
parent="great grandparent",
),
),
SingleInterval(
7,
9,
Strand.PLUS,
parent=Parent(
id="grandparent",
sequence_type="unknown",
parent="great grandparent",
),
),
),
(
Parent(
id="parent",
location=SingleInterval(3, 5, Strand.UNSTRANDED),
parent=Parent(id="grandparent", location=SingleInterval(10, 20, Strand.PLUS)),
),
SingleInterval(13, 15, Strand.UNSTRANDED, parent="grandparent"),
),
(
Parent(
id="parent",
location=SingleInterval(3, 5, Strand.UNSTRANDED),
parent=Parent(id="grandparent", location=SingleInterval(10, 20, Strand.MINUS)),
),
SingleInterval(15, 17, Strand.UNSTRANDED, parent="grandparent"),
),
],
)
def test_lift_child_location_contiguous_to_parent_single_interval(self, parent, expected):
assert parent.lift_child_location_to_parent() == expected
@pytest.mark.parametrize(
"parent,expected",
[
(
Parent(
id="parent",
location=CompoundInterval([3, 7], [5, 10], Strand.PLUS),
parent=Parent(id="grandparent", location=SingleInterval(10, 20, Strand.PLUS)),
),
CompoundInterval([13, 17], [15, 20], Strand.PLUS, parent="grandparent"),
),
(
Parent(
id="parent",
location=CompoundInterval([0, 10], [5, 15], Strand.PLUS),
sequence_type="unknown",
strand=Strand.PLUS,
parent=Parent(
id="grandparent",
location=SingleInterval(100, 200, Strand.MINUS),
),
),
CompoundInterval(
[185, 195],
[190, 200],
Strand.MINUS,
parent="grandparent",
),
),
(
Parent(
id="parent",
location=CompoundInterval([6], [9], Strand.MINUS),
parent=Parent(
id="grandparent",
location=SingleInterval(0, 10, Strand.PLUS),
sequence_type="chr",
strand=Strand.PLUS,
parent="great grandparent",
),
),
SingleInterval(
6,
9,
Strand.MINUS,
parent=Parent(
id="grandparent",
sequence_type="chr",
parent="great grandparent",
),
),
),
(
Parent(
id="parent",
sequence_type="chr",
strand=Strand.MINUS,
location=CompoundInterval([6], [8], Strand.MINUS),
parent=Parent(
id="grandparent",
sequence_type="unknown",
strand=Strand.MINUS,
location=SingleInterval(5, 15, Strand.MINUS),
parent="great grandparent",
),
),
SingleInterval(
7,
9,
Strand.PLUS,
parent=Parent(
id="grandparent",
sequence_type="unknown",
parent="great grandparent",
),
),
),
(
Parent(
id="parent",
location=CompoundInterval([3, 7], [5, 10], Strand.UNSTRANDED),
parent=Parent(id="grandparent", location=SingleInterval(10, 20, Strand.PLUS)),
),
CompoundInterval(
[13, 17],
[15, 20],
Strand.UNSTRANDED,
parent="grandparent",
),
),
(
Parent(
id="parent",
location=CompoundInterval([3], [5], Strand.UNSTRANDED),
parent=Parent(id="grandparent", location=SingleInterval(10, 20, Strand.MINUS)),
),
SingleInterval(15, 17, Strand.UNSTRANDED, parent="grandparent"),
),
],
)
def test_lift_child_location_discontiguous_to_parent_single_interval(self, parent, expected):
assert parent.lift_child_location_to_parent() == expected
@pytest.mark.parametrize(
"parent,expected_error",
[
# No location
(
Parent(parent=SingleInterval(5, 10, Strand.PLUS)),
NullParentException,
),
# Parent has no location
(
Parent(
location=SingleInterval(5, 10, Strand.PLUS),
parent="grandparent",
),
NullParentException,
),
# Location on parent can't be unstranded
(
Parent(
location=SingleInterval(5, 10, Strand.PLUS),
parent=Parent(
id="grandparent",
location=SingleInterval(0, 100, Strand.UNSTRANDED),
),
),
InvalidStrandException,
),
# Location must fit inside location on parent
(
Parent(
location=SingleInterval(5, 10, Strand.PLUS),
parent=Parent(id="grandparent", location=SingleInterval(30, 31, Strand.PLUS)),
),
ValueError,
),
],
)
def test_lift_child_location_to_parent_single_interval_error(self, parent, expected_error):
with pytest.raises(expected_error):
parent.lift_child_location_to_parent()
@pytest.mark.parametrize(
"parent,expected",
[
# Location takes up entire parent location
(
Parent(
id="parent",
location=SingleInterval(0, 10, Strand.PLUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([5, 20], [10, 25], Strand.PLUS),
),
),
CompoundInterval([5, 20], [10, 25], Strand.PLUS, parent="grandparent"),
),
# Location (unstranded) takes up part of parent location (minus)
(
Parent(
id="parent",
location=SingleInterval(10, 20, Strand.UNSTRANDED),
parent=Parent(
id="grandparent",
location=CompoundInterval([10, 20, 30], [18, 28, 38], Strand.MINUS),
),
),
CompoundInterval(
[14, 20],
[18, 26],
Strand.UNSTRANDED,
parent="grandparent",
),
),
# Location (minus) takes up one block of parent location (plus); location is at end of sequence
(
Parent(
id="parent",
location=SingleInterval(5, 10, Strand.MINUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([30, 40], [35, 45], Strand.PLUS),
),
),
SingleInterval(40, 45, Strand.MINUS, parent="grandparent"),
),
# Location (minus) takes up part of one block of parent location (minus)
(
Parent(
id="parent",
location=SingleInterval(0, 4, Strand.MINUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([30, 40], [35, 45], Strand.MINUS),
),
),
SingleInterval(41, 45, Strand.PLUS, parent="grandparent"),
),
],
)
def test_lift_child_location_contiguous_to_parent_compound_interval(self, parent, expected):
assert parent.lift_child_location_to_parent() == expected
@pytest.mark.parametrize(
"parent,expected",
[
# Location takes up entire parent location
(
Parent(
id="parent",
location=CompoundInterval([0, 5], [5, 10], Strand.PLUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([5, 20], [10, 25], Strand.PLUS),
),
),
CompoundInterval([5, 20], [10, 25], Strand.PLUS, parent="grandparent"),
),
# Location (unstranded) takes up part of parent location (minus)
(
Parent(
id="parent",
location=CompoundInterval([10, 22], [20, 23], Strand.UNSTRANDED),
parent=Parent(
id="grandparent",
location=CompoundInterval([10, 20, 30], [18, 28, 38], Strand.MINUS),
),
),
CompoundInterval(
[11, 14, 20],
[12, 18, 26],
Strand.UNSTRANDED,
parent="grandparent",
),
),
# Location (minus) takes up one block of parent location (plus); location is at end of sequence
(
Parent(
id="parent",
location=CompoundInterval([5], [10], Strand.MINUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([30, 40], [35, 45], Strand.PLUS),
),
),
SingleInterval(40, 45, Strand.MINUS, parent="grandparent"),
),
# Location (minus) takes up part of one block of parent location (minus)
(
Parent(
id="parent",
location=CompoundInterval([0, 3], [1, 4], Strand.MINUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([30, 40], [35, 45], Strand.MINUS),
),
),
CompoundInterval([41, 44], [42, 45], Strand.PLUS, parent="grandparent"),
),
],
)
def test_lift_child_location_discontiguous_to_parent_compound_interval(self, parent, expected):
assert parent.lift_child_location_to_parent() == expected
@pytest.mark.parametrize(
"parent,expected_error",
[
# Location must fit inside location on parent
(
Parent(
location=SingleInterval(5, 50, Strand.PLUS),
parent=Parent(
id="grandparent",
location=CompoundInterval([10, 20], [15, 25], Strand.PLUS),
),
),
InvalidPositionException,
),
],
)
def test_lift_child_location_to_parent_compound_interval_error(self, parent, expected_error):
with pytest.raises(expected_error):
parent.lift_child_location_to_parent()
@pytest.mark.parametrize(
"parent,location,expected",
[
(
Parent(),
SingleInterval(5, 10, Strand.PLUS),
Parent(location=SingleInterval(5, 10, Strand.PLUS), strand=Strand.PLUS),
),
(
Parent(
id="parent",
sequence_type="unknown",
strand=Strand.MINUS,
location=SingleInterval(0, 2, Strand.MINUS),
sequence=Sequence("AAA", Alphabet.NT_STRICT),
),
SingleInterval(2, 3, Strand.PLUS),
Parent(
id="parent",
sequence_type="unknown",
strand=Strand.PLUS,
location=SingleInterval(2, 3, Strand.PLUS),
sequence=Sequence("AAA", Alphabet.NT_STRICT),
),
),
(
Parent(
id="parent",
sequence_type="unknown",
strand=Strand.MINUS,
location=SingleInterval(0, 2, Strand.MINUS),
sequence=Sequence("AAA", Alphabet.NT_STRICT),
),
None,
Parent(
id="parent",
sequence_type="unknown",
sequence=Sequence("AAA", Alphabet.NT_STRICT),
),
),
],
)
def test_reset_location(self, parent, location, expected):
assert parent.reset_location(location) == expected
@pytest.mark.parametrize(
"parent,location,expected_exception",
[
(
Parent(sequence=Sequence("AAA", Alphabet.NT_STRICT)),
SingleInterval(0, 5, Strand.PLUS),
InvalidPositionException,
),
(
Parent(id="id1", sequence=Sequence("AAA", Alphabet.NT_STRICT)),
SingleInterval(
0,
1,
Strand.PLUS,
parent=Parent(id="id2", sequence=Sequence("AAA", Alphabet.NT_STRICT)),
),
ParentException,
),
],
)
def test_reset_location_error(self, parent, location, expected_exception):
with pytest.raises(expected_exception):
parent.reset_location(location)
@pytest.mark.parametrize(
"parent,sequence,include_self,expected",
[
(Parent(), Sequence("AA", Alphabet.NT_STRICT), True, False),
(Parent(), Sequence("AA", Alphabet.NT_STRICT), False, False),
(
Parent(sequence=Sequence("AA", Alphabet.NT_STRICT)),
Sequence("AA", Alphabet.NT_STRICT),
True,
True,
),
(
Parent(sequence=Sequence("AA", Alphabet.NT_STRICT)),
Sequence("AA", Alphabet.NT_STRICT),
False,
False,
),
(
Parent(
sequence=Sequence("AA", Alphabet.NT_STRICT),
parent=Sequence("AA", Alphabet.NT_STRICT),
),
Sequence("AA", Alphabet.NT_STRICT),
False,
True,
),
(
Parent(
sequence=Sequence("AA", Alphabet.NT_STRICT),
parent=Sequence("AAT", Alphabet.NT_STRICT),
),
Sequence("AAT", Alphabet.NT_STRICT),
False,
True,
),
(
Parent(
sequence=Sequence("AA", Alphabet.NT_STRICT),
parent=Sequence("AAT", Alphabet.NT_STRICT),
),
Sequence("AAT", Alphabet.NT_STRICT, id="id"),
True,
False,
),
(
Parent(
parent=Parent(parent=Parent(parent=Parent(sequence=Sequence("AAA", Alphabet.NT_STRICT, id="seq"))))
),
Sequence("AAA", Alphabet.NT_STRICT, id="seq"),
True,
True,
),
],
)
def test_has_ancestor_sequence(self, parent, sequence, include_self, expected):
assert parent.has_ancestor_sequence(sequence, include_self) == expected
def test_id(self, id, location, sequence, expected):
assert Parent(id=id, location=location, sequence=sequence).id == expected
def test_sequence_type(self, sequence_type, location, sequence, expected):
assert Parent(sequence_type=sequence_type, location=location, sequence=sequence).sequence_type == expected
def test_strand(self, strand, location, sequence, expected):
assert Parent(strand=strand, location=location, sequence=sequence).strand == expected
class TestSequence:
def test_init(self):
sequence = Sequence(
"ACTG",
Alphabet.NT_STRICT,
id="id",
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
location=SingleInterval(5, 9, Strand.MINUS, parent="parent"),
),
)
# Sequence data
assert sequence.sequence == Seq("ACTG")
assert str(sequence) == "ACTG"
# Alphabet
assert sequence.alphabet == Alphabet.NT_STRICT
# ID
assert sequence.id == "id"
# Sequence type
assert sequence.sequence_type == "seqtype_1"
# Parent ID
assert sequence.parent_id == "parent"
assert Sequence("A", Alphabet.NT_STRICT,
parent="parent").parent_id == "parent"
assert (Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(
location=SingleInterval(5, 6, Strand.MINUS, parent="parent")),
).parent_id == "parent")
assert Sequence("A", Alphabet.NT_STRICT).parent_id is None
# Parent type
assert sequence.parent_type == "seqtype_2"
# Parent strand
assert sequence.parent_strand == Strand.MINUS
assert Sequence(
"A", Alphabet.NT_STRICT,
parent=Strand.UNSTRANDED).parent_strand == Strand.UNSTRANDED
# Location on parent
assert (Sequence(
"A",
Alphabet.NT_STRICT,
parent=SingleInterval(3, 4, Strand.UNSTRANDED),
).parent_strand == Strand.UNSTRANDED)
assert Sequence("A", Alphabet.NT_STRICT).parent_strand is None
assert sequence.location_on_parent == SingleInterval(5,
9,
Strand.MINUS,
parent="parent")
# No alphabet validation
Sequence("xxx", Alphabet.NT_STRICT, validate_alphabet=False)
@pytest.mark.parametrize(
"data,alphabet,parent_id,parent_type,parent_strand,location_on_parent,expected_exception",
[
("A-C", Alphabet.NT_STRICT, None, None, None, None, AlphabetError),
(
"ACG",
Alphabet.NT_STRICT,
None,
None,
None,
SingleInterval(0, 4, Strand.PLUS),
ParentException,
),
(
"ATT",
Alphabet.NT_STRICT,
"parent1",
None,
None,
SingleInterval(0, 3, Strand.PLUS, parent="parent2"),
ParentException,
),
(
"GGG",
Alphabet.NT_STRICT,
None,
None,
Strand.MINUS,
SingleInterval(0, 3, Strand.PLUS),
InvalidStrandException,
),
(
"GGG",
Alphabet.NT_STRICT,
None,
"seqtype_2",
None,
SingleInterval(
0,
3,
Strand.PLUS,
parent=Parent(sequence_type="seqtype_3"),
),
ParentException,
),
],
)
def test_init_invalid_params(
self,
data,
alphabet,
parent_id,
parent_type,
parent_strand,
location_on_parent,
expected_exception,
):
with pytest.raises(expected_exception):
Sequence(
data,
alphabet,
parent=Parent(
id=parent_id,
sequence_type=parent_type,
strand=parent_strand,
location=location_on_parent,
),
)
@pytest.mark.parametrize(
"sequence,other,expected",
[
(
Sequence("AAAA", Alphabet.NT_STRICT, validate_alphabet=False),
"AAAA",
False,
),
(
Sequence("AAAA", Alphabet.NT_STRICT, validate_alphabet=False),
Sequence("AAAA", Alphabet.NT_STRICT, validate_alphabet=True),
True,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
True,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
Sequence(
"AAAa",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
False,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
Sequence(
"AAAA",
Alphabet.NT_EXTENDED,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
False,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq2",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
False,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype_1",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype_2",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
False,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.PLUS, None),
validate_alphabet=False,
),
Sequence(
"AAAA",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype",
parent=SingleInterval(0, 4, Strand.UNSTRANDED, None),
validate_alphabet=False,
),
False,
),
(
Sequence("AAAA", Alphabet.NT_STRICT, parent="parent1"),
Sequence("AAAA", Alphabet.NT_STRICT, parent="parent2"),
False,
),
(
Sequence("AAAA", Alphabet.NT_STRICT, parent="parent"),
Sequence("AAAA", Alphabet.NT_STRICT),
False,
),
(
Sequence("AAAA", Alphabet.NT_STRICT, parent=Strand.UNSTRANDED),
Sequence("AAAA", Alphabet.NT_STRICT, parent=Strand.PLUS),
False,
),
(
Sequence("AAAA", Alphabet.NT_STRICT, parent=Strand.UNSTRANDED),
Sequence("AAAA", Alphabet.NT_STRICT),
False,
),
(
Sequence(
"AAAA",
Alphabet.NT_STRICT,
parent="seqtype",
),
Sequence("AAAA", Alphabet.NT_STRICT),
False,
),
],
)
def test_equals(self, sequence, other, expected):
assert (sequence == other) is expected
assert (other == sequence) is expected
def test_str(self):
assert str(Sequence("AAAAt", Alphabet.NT_EXTENDED_GAPPED)) == "AAAAt"
def test_len(self):
assert len(Sequence("", Alphabet.NT_EXTENDED_GAPPED)) == 0
assert len(Sequence("AAAAt", Alphabet.NT_EXTENDED_GAPPED)) == 5
@pytest.mark.parametrize(
"seq,key,exp",
[
# No parent
(Sequence("acgtacgt", Alphabet.NT_STRICT), 3,
Sequence("t", Alphabet.NT_STRICT)),
(Sequence("acgtacgt", Alphabet.NT_STRICT), slice(
3, 6), Sequence("tac", Alphabet.NT_STRICT)),
(Sequence("acgtacgt", Alphabet.NT_STRICT), slice(
3, 10), Sequence("tacgt", Alphabet.NT_STRICT)),
# Parent with location; slice
(
Sequence("actgactg",
Alphabet.NT_STRICT,
parent=SingleInterval(0, 8, Strand.PLUS)),
slice(3, 6),
Sequence("gac",
Alphabet.NT_STRICT,
parent=SingleInterval(3, 6, Strand.PLUS)),
),
(
Sequence("actgactg",
Alphabet.NT_STRICT,
parent=SingleInterval(0, 8, Strand.MINUS)),
slice(3, 6),
Sequence("gac",
Alphabet.NT_STRICT,
parent=SingleInterval(2, 5, Strand.MINUS)),
),
# Parent with location; single position
(
Sequence("actgactg",
Alphabet.NT_STRICT,
parent=SingleInterval(0, 8, Strand.PLUS)),
3,
Sequence("g",
Alphabet.NT_STRICT,
parent=SingleInterval(3, 4, Strand.PLUS)),
),
(
Sequence("actgactg",
Alphabet.NT_STRICT,
parent=SingleInterval(0, 8, Strand.MINUS)),
3,
Sequence("g",
Alphabet.NT_STRICT,
parent=SingleInterval(4, 5, Strand.MINUS)),
),
# Parent without full location
(
Sequence("actgactg", Alphabet.NT_STRICT, parent="parent"),
slice(3, 6),
Sequence("gac", Alphabet.NT_STRICT, parent="parent"),
),
(
Sequence(
"actgactg", Alphabet.NT_STRICT, parent=Strand.UNSTRANDED),
slice(3, 6),
Sequence("gac", Alphabet.NT_STRICT, parent=Strand.UNSTRANDED),
),
],
)
def test_getitem(self, seq, key, exp):
assert seq[key] == exp
def test_getitem_error(self):
with pytest.raises(InvalidStrandException):
Sequence("actgactg",
Alphabet.NT_STRICT,
parent=SingleInterval(0, 8, Strand.UNSTRANDED))[3:6]
@pytest.mark.parametrize(
"sequence,alphabet,validate_alphabet",
[
("", Alphabet.NT_STRICT, True),
("acgtACGT", Alphabet.NT_STRICT, True),
("N", Alphabet.NT_STRICT, False),
("acNNNw", Alphabet.NT_EXTENDED, True),
("AN-", Alphabet.NT_EXTENDED, False),
("GG--AAA", Alphabet.NT_STRICT_GAPPED, True),
("AN-", Alphabet.NT_STRICT_GAPPED, False),
("nnAAw-cg", Alphabet.NT_EXTENDED_GAPPED, True),
("xxx", Alphabet.NT_EXTENDED_GAPPED, False),
("MWT*", Alphabet.AA, True),
("T*-", Alphabet.AA, False),
("ABCDE-", Alphabet.GENERIC, True),
("*", Alphabet.GENERIC, False),
],
)
def test_validate_alphabet(self, sequence, alphabet, validate_alphabet):
Sequence(sequence, alphabet, validate_alphabet=validate_alphabet)
@pytest.mark.parametrize(
"sequence,alphabet",
[
("N", Alphabet.NT_STRICT),
("A-", Alphabet.NT_EXTENDED),
("AN-", Alphabet.NT_STRICT_GAPPED),
("E", Alphabet.NT_EXTENDED_GAPPED),
("R-", Alphabet.AA),
("?", Alphabet.GENERIC),
],
)
def test_validate_alphabet_error(self, sequence, alphabet):
with pytest.raises(AlphabetError):
Sequence(sequence, alphabet, validate_alphabet=True)
@pytest.mark.parametrize(
"sequence,expected",
[
(Sequence("A", Alphabet.NT_STRICT, parent="parent"), "parent"),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(id="parent",
location=SingleInterval(
10, 11, Strand.UNSTRANDED)),
),
"parent",
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
location=SingleInterval(
10, 11, Strand.UNSTRANDED, parent="parent"),
),
),
"parent",
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(location=SingleInterval(
10, 11, Strand.UNSTRANDED, parent="parent")),
),
"parent",
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=SingleInterval(10, 11, Strand.UNSTRANDED),
),
None,
),
(Sequence("A", Alphabet.NT_STRICT), None),
],
)
def test_parent_id(self, sequence, expected):
assert sequence.parent_id == expected
@pytest.mark.parametrize(
"sequence,expected",
[
(Sequence("A", Alphabet.NT_STRICT), None),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(sequence_type="seqtype"),
),
"seqtype",
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(location=SingleInterval(
0,
1,
Strand.PLUS,
parent=Parent(sequence_type="seqtype"),
)),
),
"seqtype",
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(location=SingleInterval(
0,
1,
Strand.PLUS,
parent=Sequence(
"AA", Alphabet.NT_STRICT, type="seqtype"),
)),
),
"seqtype",
),
],
)
def test_parent_type(self, sequence, expected):
assert sequence.parent_type == expected
@pytest.mark.parametrize(
"sequence,expected",
[
(Sequence("A", Alphabet.NT_STRICT), None),
(
Sequence("A", Alphabet.NT_STRICT, parent=Strand.MINUS),
Strand.MINUS,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=SingleInterval(10, 11, Strand.MINUS),
),
Strand.MINUS,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=SingleInterval(10, 11, Strand.MINUS),
),
Strand.MINUS,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
parent=Parent(
strand=Strand.MINUS,
location=SingleInterval(10, 11, Strand.MINUS),
),
),
Strand.MINUS,
),
],
)
def test_parent_strand(self, sequence, expected):
assert sequence.parent_strand == expected
@pytest.mark.parametrize(
"sequence,new_id,new_type,expected",
[
(
Sequence("", Alphabet.NT_STRICT),
None,
None,
Sequence("", Alphabet.NT_STRICT),
),
(
Sequence("ACGtacgT", Alphabet.NT_STRICT),
None,
None,
Sequence("AcgtaCGT", Alphabet.NT_STRICT),
),
(
Sequence("ATUGCYRSWKMBdhvnNVHDbmkwsrycguta",
Alphabet.NT_EXTENDED),
None,
None,
Sequence("taacgryswmkvHDBNnbdhVKMWSYRGCAAT",
Alphabet.NT_EXTENDED),
),
(
Sequence("--A-CGta", Alphabet.NT_STRICT_GAPPED),
None,
None,
Sequence("taCG-T--", Alphabet.NT_STRICT_GAPPED),
),
(
Sequence("AtUC-N-", Alphabet.NT_EXTENDED_GAPPED),
None,
None,
Sequence("-N-GAaT", Alphabet.NT_EXTENDED_GAPPED),
),
(
Sequence("ACGta", Alphabet.NT_STRICT),
"new_id",
"seqtype",
Sequence(
"taCGT",
Alphabet.NT_STRICT,
id="new_id",
type="seqtype",
),
),
(
Sequence("ACGta", Alphabet.NT_STRICT, parent=Strand.PLUS),
None,
None,
Sequence("taCGT", Alphabet.NT_STRICT, parent=Strand.MINUS),
),
(
Sequence(
"ACGta",
Alphabet.NT_STRICT,
parent=SingleInterval(5, 10, Strand.PLUS),
),
None,
None,
Sequence(
"taCGT",
Alphabet.NT_STRICT,
parent=SingleInterval(5, 10, Strand.MINUS),
),
),
],
)
def test_reverse_complement(self, sequence, new_id, new_type, expected):
assert sequence.reverse_complement(new_id=new_id,
new_type=new_type) == expected
@pytest.mark.parametrize(
"sequence",
[
Sequence("AAA", Alphabet.AA),
Sequence("AAA", Alphabet.GENERIC),
Sequence("xxx", Alphabet.NT_STRICT, validate_alphabet=False),
],
)
def test_reverse_complement_error(self, sequence):
with pytest.raises(AlphabetError):
sequence.reverse_complement()
@pytest.mark.parametrize(
"seq1,seq2,new_id,data_only,expected",
[
(
Sequence("", Alphabet.NT_STRICT, parent="parent1"),
Sequence("", Alphabet.NT_STRICT, parent="parent2"),
"new_id",
True,
Sequence("", Alphabet.NT_STRICT, id="new_id"),
),
(
Sequence("AA", Alphabet.NT_STRICT, parent="parent1"),
Sequence("TT", Alphabet.NT_STRICT, parent="parent2"),
"new_id",
True,
Sequence("AATT", Alphabet.NT_STRICT, id="new_id"),
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
type="seqtype_1",
parent=Parent(
id="parent1",
strand=Strand.PLUS,
location=SingleInterval(5, 7, Strand.PLUS),
),
),
Sequence(
"TT",
Alphabet.NT_STRICT,
type="seqtype_2",
parent=Parent(
id="parent1",
strand=Strand.MINUS,
location=SingleInterval(20, 22, Strand.MINUS),
),
),
None,
True,
Sequence("AATT", Alphabet.NT_STRICT),
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(
id="parent1",
strand=Strand.PLUS,
location=SingleInterval(5, 7, Strand.PLUS),
),
),
Sequence(
"TT",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(id="parent1", strand=Strand.PLUS),
),
None,
False,
Sequence(
"AATT",
Alphabet.NT_STRICT,
type="seqtype",
parent="parent1",
),
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(id="parent1", strand=Strand.PLUS),
),
Sequence(
"TT",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(
id="parent1",
strand=Strand.PLUS,
location=SingleInterval(5, 7, Strand.PLUS),
),
),
None,
False,
Sequence(
"AATT",
Alphabet.NT_STRICT,
type="seqtype",
parent="parent1",
),
),
(
Sequence(
"CC",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(id="parent",
location=SingleInterval(3, 5, Strand.PLUS)),
),
Sequence(
"TT",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(id="parent",
location=SingleInterval(10, 12,
Strand.PLUS)),
),
"new_id",
True,
Sequence("CCTT", Alphabet.NT_STRICT, id="new_id"),
),
(
Sequence(
"CC",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(id="parent",
location=SingleInterval(3, 5, Strand.PLUS)),
),
Sequence(
"TT",
Alphabet.NT_STRICT,
type="seqtype",
parent=Parent(id="parent",
location=SingleInterval(0, 2, Strand.PLUS)),
),
"new_id",
True,
Sequence("CCTT", Alphabet.NT_STRICT, id="new_id"),
),
(
Sequence("AA", Alphabet.NT_STRICT, id="seq1", parent="parent"),
Sequence("", Alphabet.NT_STRICT, id="seq2", parent="parent"),
None,
False,
Sequence("AA", Alphabet.NT_STRICT, parent="parent"),
),
(
Sequence(
"ACT",
Alphabet.NT_STRICT,
parent=Parent(id="parent",
location=SingleInterval(2, 5, Strand.PLUS)),
),
Sequence(
"GGA",
Alphabet.NT_STRICT,
parent=Parent(id="parent",
location=SingleInterval(8, 11, Strand.PLUS)),
),
"new_id",
False,
Sequence(
"ACTGGA",
Alphabet.NT_STRICT,
id="new_id",
parent=Parent(
id="parent",
location=CompoundInterval.from_single_intervals([
SingleInterval(2, 5, Strand.PLUS),
SingleInterval(8, 11, Strand.PLUS),
]),
),
),
),
(
Sequence(
"ACT",
Alphabet.NT_STRICT,
parent=Parent(id="parent",
location=SingleInterval(8, 11,
Strand.MINUS)),
),
Sequence(
"GGA",
Alphabet.NT_STRICT,
parent=Parent(id="parent",
location=SingleInterval(2, 5, Strand.MINUS)),
),
"new_id",
False,
Sequence(
"ACTGGA",
Alphabet.NT_STRICT,
id="new_id",
parent=Parent(
id="parent",
location=CompoundInterval.from_single_intervals([
SingleInterval(2, 5, Strand.MINUS),
SingleInterval(8, 11, Strand.MINUS),
]),
),
),
),
(
Sequence(
"ACT",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
strand=Strand.PLUS,
location=SingleInterval(5, 8, Strand.PLUS),
),
),
Sequence(
"GCG",
Alphabet.NT_STRICT,
id="seq1",
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
strand=Strand.PLUS,
location=SingleInterval(15, 18, Strand.PLUS),
),
),
None,
False,
Sequence(
"ACTGCG",
Alphabet.NT_STRICT,
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
strand=Strand.PLUS,
location=CompoundInterval.from_single_intervals([
SingleInterval(5, 8, Strand.PLUS),
SingleInterval(15, 18, Strand.PLUS),
]),
),
),
),
],
)
def test_append(self, seq1, seq2, new_id, data_only, expected):
assert seq1.append(seq2, new_id, data_only) == expected
@pytest.mark.parametrize(
"seq1,seq2,new_id,data_only",
[
(
Sequence("AA", Alphabet.NT_STRICT),
Sequence("TT", Alphabet.NT_EXTENDED),
None,
True,
),
(
Sequence("AA", Alphabet.NT_STRICT, type="seqtype_1"),
Sequence("AA", Alphabet.NT_STRICT, type="seqtype_2"),
None,
False,
),
(
Sequence("AA", Alphabet.NT_STRICT, parent="parent1"),
Sequence("AA", Alphabet.NT_STRICT, parent="parent2"),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(10, 12, Strand.PLUS),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(5, 7, Strand.PLUS),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(2, 4, Strand.MINUS),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(5, 7, Strand.MINUS),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(10, 12, Strand.PLUS),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(11, 13, Strand.PLUS),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(10, 12, Strand.UNSTRANDED),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=SingleInterval(15, 17, Strand.UNSTRANDED),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent1",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent2",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype_1",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype_2",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype",
strand=Strand.MINUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent",
),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAAT", Alphabet.NT_STRICT),
parent="grandparent",
),
),
None,
False,
),
(
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent1",
),
),
Sequence(
"AA",
Alphabet.NT_STRICT,
parent=Parent(
id="parent",
sequence_type="seqtype",
strand=Strand.PLUS,
sequence=Sequence("AAA", Alphabet.NT_STRICT),
parent="grandparent2",
),
),
None,
False,
),
],
)
def test_append_error(self, seq1, seq2, new_id, data_only):
with pytest.raises(ValueError):
seq1.append(seq2, new_id, data_only)
@pytest.mark.parametrize(
"sequence,sequence_type,include_self,expected",
[
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
True,
Parent(sequence=Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
)),
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
False,
Parent(id="parent", sequence_type="seqtype"),
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent",
sequence_type="seqtype_2"),
),
),
"seqtype_2",
True,
Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent", sequence_type="seqtype_2"),
),
),
],
)
def test_first_ancestor_of_type(self, sequence, sequence_type,
include_self, expected):
assert sequence.first_ancestor_of_type(
sequence_type, include_self=include_self) == expected
@pytest.mark.parametrize(
"sequence,sequence_type,include_self",
[
(
Sequence("A", Alphabet.NT_STRICT, id="self"),
"seqtype_1",
True,
),
(
Sequence("A", Alphabet.NT_STRICT, id="self", parent="parent"),
"seqtype_1",
True,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype_2",
parent=Parent(
id="parent",
sequence_type="seqtype_1",
parent=Parent(id="grandparent",
sequence_type="seqtype_1"),
),
),
"seqtype_3",
True,
),
],
)
def test_first_ancestor_of_type_error(self, sequence, sequence_type,
include_self):
with pytest.raises(NoSuchAncestorException):
sequence.first_ancestor_of_type(sequence_type,
include_self=include_self)
@pytest.mark.parametrize(
"sequence,sequence_type,include_self,expected",
[
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
True,
True,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype",
parent=Parent(id="parent", sequence_type="seqtype"),
),
"seqtype",
False,
True,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype_1",
parent=Parent(
id="parent",
sequence_type="seqtype_2",
parent=Parent(id="grandparent",
sequence_type="seqtype_2"),
),
),
"seqtype_2",
True,
True,
),
(
Sequence("A", Alphabet.NT_STRICT, id="self"),
"seqtype_1",
True,
False,
),
(
Sequence("A", Alphabet.NT_STRICT, id="self", parent="parent"),
"seqtype_1",
True,
False,
),
(
Sequence(
"A",
Alphabet.NT_STRICT,
id="self",
type="seqtype_2",
parent=Parent(
id="parent",
sequence_type="seqtype_1",
parent=Parent(id="grandparent",
sequence_type="seqtype_1"),
),
),
"seqtype_3",
True,
False,
),
],
)
def test_has_ancestor_of_type(self, sequence, sequence_type, include_self,
expected):
assert sequence.has_ancestor_of_type(
sequence_type, include_self=include_self) is expected
@pytest.mark.parametrize(
"sequence,expected",
[
(Sequence("ATGCATATTTGGAAACCAA", Alphabet.NT_STRICT,
id="test"), ">test\nATGCATATTT\nGGAAACCAA"),
(Sequence("ATGCATATTTGGAAACCAA",
Alphabet.NT_STRICT), ">None\nATGCATATTT\nGGAAACCAA"),
(Sequence("GGAAACCAA", Alphabet.NT_STRICT,
id="test"), ">test\nGGAAACCAA"),
(
Sequence("ATGCATATTTGGAAACCAAGGAAACCAA",
Alphabet.NT_STRICT,
id="test"),
">test\nATGCATATTT\nGGAAACCAAG\nGAAACCAA",
),
(
Sequence(
data="AAAAAAA",
alphabet=Alphabet.NT_STRICT,
id="test",
parent=Parent(
location=SingleInterval(33, 40, Strand.MINUS)),
),
">test\nAAAAAAA",
),
],
)
def test_to_fasta(self, sequence, expected):
s_fa = sequence.to_fasta(num_chars=10)
assert s_fa == expected
def test_empty_to_fasta(self):
s = Sequence("", Alphabet.NT_STRICT)
with pytest.raises(EmptySequenceFastaError):
s.to_fasta()
def _(obj) -> Parent:
return Parent(sequence=obj)
def test_location(self):
assert Parent(location=SingleInterval(0, 1, Strand.PLUS)).location == SingleInterval(0, 1, Strand.PLUS)
def test_sequence(self):
assert Parent(sequence=Sequence("A", Alphabet.NT_STRICT)).sequence == Sequence("A", Alphabet.NT_STRICT)
def test_require_parent_has_parent(self):
with pytest.raises(NullParentException):
ObjectValidation.require_parent_has_parent(Parent(id="parent"))
ObjectValidation.require_parent_has_parent(
Parent(id="parent", parent="grandparent"))
