diff --git a/pyhmmer/easel.pyi b/pyhmmer/easel.pyi
index c3fbe8762bd500fec7bdf1e5abdc415cf8a53cf1..ddebcb358913581947c4e4121fe9fe20faac9ff2 100644
--- a/pyhmmer/easel.pyi
+++ b/pyhmmer/easel.pyi
@@ -582,7 +582,7 @@ class DigitalSequence(Sequence):
# --- Sequence block ---------------------------------------------------------
-S = typing.TypeVar("S", bound=Sequence)
+S = typing.TypeVar("S", TextSequence, DigitalSequence)
B = typing.TypeVar("B")
class SequenceBlock(typing.MutableSequence[S], typing.Generic[S]):
@@ -626,7 +626,7 @@ class DigitalSequenceBlock(SequenceBlock[DigitalSequence]):
# --- Sequence File ----------------------------------------------------------
-class SequenceFile(typing.ContextManager[SequenceFile], typing.Iterator[Sequence]):
+class SequenceFile(typing.Generic[S], typing.ContextManager[SequenceFile[S]], typing.Iterator[S]):
_FORMATS: typing.ClassVar[typing.Dict[str, int]]
alphabet: typing.Optional[Alphabet]
name: typing.Optional[str]
@@ -636,24 +636,35 @@ class SequenceFile(typing.ContextManager[SequenceFile], typing.Iterator[Sequence
) -> Sequence: ...
@classmethod
def parseinto(cls, seq: Sequence, buffer: BUFFER, format: str) -> Sequence: ...
+ @typing.overload
def __init__(
- self,
+ self: SequenceFile[DigitalSequence],
file: typing.Union[typing.AnyStr, os.PathLike[typing.AnyStr], typing.BinaryIO],
format: typing.Optional[str] = None,
*,
ignore_gaps: bool = False,
- digital: bool = False,
+ digital: Literal[True],
+ alphabet: typing.Optional[Alphabet] = None,
+ ) -> None: ...
+ @typing.overload
+ def __init__(
+ self: SequenceFile[TextSequence],
+ file: typing.Union[typing.AnyStr, os.PathLike[typing.AnyStr], typing.BinaryIO],
+ format: typing.Optional[str] = None,
+ *,
+ ignore_gaps: bool = False,
+ digital: Literal[False] = False,
alphabet: typing.Optional[Alphabet] = None,
) -> None: ...
- def __enter__(self) -> SequenceFile: ...
+ def __enter__(self) -> SequenceFile[S]: ...
def __exit__(
self,
exc_type: typing.Optional[typing.Type[BaseException]],
exc_value: typing.Optional[BaseException],
traceback: typing.Optional[types.TracebackType],
) -> bool: ...
- def __iter__(self) -> SequenceFile: ...
- def __next__(self) -> Sequence: ...
+ def __iter__(self) -> SequenceFile[S]: ...
+ def __next__(self) -> S: ...
def __repr__(self) -> str: ...
@property
def closed(self) -> bool: ...
@@ -663,15 +674,15 @@ class SequenceFile(typing.ContextManager[SequenceFile], typing.Iterator[Sequence
def format(self) -> str: ...
def read(
self, skip_info: bool = False, skip_sequence: bool = False
- ) -> typing.Optional[Sequence]: ...
+ ) -> typing.Optional[S]: ...
def readinto(
self, seq: Sequence, skip_info: bool = False, skip_sequence: bool = False
- ) -> typing.Optional[Sequence]: ...
+ ) -> typing.Optional[S]: ...
def read_block(
self,
sequences: typing.Optional[int] = None,
residues: typing.Optional[int] = None,
- ) -> SequenceBlock[Sequence]: ...
+ ) -> SequenceBlock[S]: ...
def rewind(self) -> None: ...
def close(self) -> None: ...
def guess_alphabet(self) -> typing.Optional[Alphabet]: ...
diff --git a/pyhmmer/hmmer.py b/pyhmmer/hmmer.py
index ba0d0ab9657c922df254603e9e1c8b8d9bb24444..7b7641918f0bfa856e0546fbcefdbadb9c1a4491 100644
--- a/pyhmmer/hmmer.py
+++ b/pyhmmer/hmmer.py
@@ -291,7 +291,7 @@ class _BaseWorker(typing.Generic[_Q, _T, _R], threading.Thread):
class _SEARCHWorker(
_BaseWorker[
_SEARCHQueryType,
- typing.Union[DigitalSequenceBlock, SequenceFile],
+ typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
"TopHits[_SEARCHQueryType]",
]
):
@@ -311,7 +311,7 @@ class _SEARCHWorker(
class _PHMMERWorker(
_BaseWorker[
_PHMMERQueryType,
- typing.Union[DigitalSequenceBlock, SequenceFile],
+ typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
"TopHits[_PHMMERQueryType]",
]
):
@@ -425,7 +425,7 @@ class _JACKHMMERWorker(
class _NHMMERWorker(
_BaseWorker[
_NHMMERQueryType,
- typing.Union[DigitalSequenceBlock, SequenceFile],
+ typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
"TopHits[_NHMMERQueryType]",
]
):
@@ -594,7 +594,7 @@ class _BaseDispatcher(typing.Generic[_Q, _T, _R], abc.ABC):
class _SEARCHDispatcher(
_BaseDispatcher[
_SEARCHQueryType,
- typing.Union[DigitalSequenceBlock, SequenceFile],
+ typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
"TopHits[_SEARCHQueryType]",
]
):
@@ -628,7 +628,7 @@ class _SEARCHDispatcher(
class _PHMMERDispatcher(
_BaseDispatcher[
_PHMMERQueryType,
- typing.Union[DigitalSequenceBlock, SequenceFile],
+ typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
"TopHits[_PHMMERQueryType]",
]
):
@@ -724,14 +724,14 @@ class _JACKHMMERDispatcher(
class _NHMMERDispatcher(
_BaseDispatcher[
_NHMMERQueryType,
- typing.Union[DigitalSequenceBlock, SequenceFile],
+ typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
"TopHits[_NHMMERQueryType]",
]
):
def __init__(
self,
queries: typing.Iterable[_NHMMERQueryType],
- targets: typing.Union[DigitalSequenceBlock, SequenceFile],
+ targets: typing.Union[DigitalSequenceBlock, "SequenceFile[DigitalSequence]"],
cpus: int = 0,
callback: typing.Optional[
typing.Callable[[_NHMMERQueryType, int], None]
@@ -813,7 +813,7 @@ class _SCANDispatcher(
def hmmsearch(
queries: typing.Union[_P, typing.Iterable[_P]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Iterable[DigitalSequence],
*,
cpus: int = 0,
callback: typing.Optional[typing.Callable[[_P, int], None]] = None,
@@ -895,7 +895,7 @@ def hmmsearch(
raise ValueError("expected digital mode `SequenceFile` for targets")
assert sequences.alphabet is not None
alphabet = alphabet or sequences.alphabet
- targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequences
+ targets: typing.Union["SequenceFile[DigitalSequence]", DigitalSequenceBlock] = sequences
elif isinstance(sequences, DigitalSequenceBlock):
alphabet = alphabet or sequences.alphabet
targets = sequences
@@ -927,7 +927,7 @@ def hmmsearch(
def phmmer(
queries: typing.Union[_M, typing.Iterable[_M]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Iterable[DigitalSequence],
*,
cpus: int = 0,
callback: typing.Optional[typing.Callable[[_M, int], None]] = None,
@@ -987,14 +987,13 @@ def phmmer(
queries = (queries,)
if isinstance(sequences, SequenceFile):
- sequence_file: SequenceFile = sequences
- if sequence_file.name is None:
+ if sequences.name is None:
raise ValueError("expected named `SequenceFile` for targets")
- if not sequence_file.digital:
+ if not sequences.digital:
raise ValueError("expected digital mode `SequenceFile` for targets")
- assert sequence_file.alphabet is not None
- alphabet = alphabet or sequence_file.alphabet
- targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequence_file
+ assert sequences.alphabet is not None
+ alphabet = alphabet or sequences.alphabet
+ targets: typing.Union["SequenceFile[DigitalSequence]", DigitalSequenceBlock] = sequences
elif isinstance(sequences, DigitalSequenceBlock):
alphabet = alphabet or sequences.alphabet
targets = sequences
@@ -1027,7 +1026,7 @@ def phmmer(
@typing.overload
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Iterable[DigitalSequence],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1043,7 +1042,7 @@ def jackhmmer(
@typing.overload
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Iterable[DigitalSequence],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1059,7 +1058,7 @@ def jackhmmer(
@typing.overload
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], "SequenceFile[DigitalSequence]"],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1076,7 +1075,7 @@ def jackhmmer(
def jackhmmer(
queries: typing.Union[_JACKHMMERQueryType, typing.Iterable[_JACKHMMERQueryType]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Union[typing.Iterable[DigitalSequence], "SequenceFile[DigitalSequence]"],
*,
max_iterations: typing.Optional[int] = 5,
select_hits: typing.Optional[typing.Callable[["TopHits[_JACKHMMERQueryType]"], None]] = None,
@@ -1209,7 +1208,7 @@ def jackhmmer(
def nhmmer(
queries: typing.Union[_N, typing.Iterable[_N]],
- sequences: typing.Union[typing.Iterable[DigitalSequence], SequenceFile],
+ sequences: typing.Iterable[DigitalSequence],
*,
cpus: int = 0,
callback: typing.Optional[typing.Callable[[_N, int], None]] = None,
@@ -1279,7 +1278,7 @@ def nhmmer(
raise ValueError("expected digital mode `SequenceFile` for targets")
assert sequences.alphabet is not None
alphabet = alphabet or sequences.alphabet
- targets: typing.Union[SequenceFile, DigitalSequenceBlock] = sequences
+ targets: typing.Union["SequenceFile[DigitalSequence]", DigitalSequenceBlock] = sequences
elif isinstance(sequences, DigitalSequenceBlock):
alphabet = alphabet or sequences.alphabet
targets = sequences
@@ -1625,7 +1624,7 @@ if __name__ == "__main__":
sequences = sequences.read_block() # type: ignore
# load the query sequences iteratively
with SequenceFile(args.seqfile, digital=True, alphabet=alphabet) as queries:
- hits_list = phmmer(queries, sequences, cpus=args.jobs) # type: ignore
+ hits_list = phmmer(queries, sequences, cpus=args.jobs)
for hits in hits_list:
for hit in hits:
if hit.reported:
@@ -1646,7 +1645,7 @@ if __name__ == "__main__":
def open_query_file(
queryfile: typing.Union["os.PathLike[str]", typing.BinaryIO],
alphabet: Alphabet,
- ) -> typing.Iterator[typing.Union[SequenceFile, HMMFile]]:
+ ) -> typing.Iterator[typing.Union["SequenceFile[DigitalSequence]", HMMFile]]:
"""Open either a sequence file or an HMM file."""
try:
yield SequenceFile(queryfile, digital=True, alphabet=alphabet)
@@ -1691,7 +1690,7 @@ if __name__ == "__main__":
# at the moment `LongTargetsPipeline` only support block targets, not files
with SequenceFile(args.seqdb, digital=True) as seqfile:
with SequenceFile(args.seqfile, digital=True) as queryfile:
- hits_list = nhmmer(queryfile, seqfile, cpus=args.jobs) # type: ignore
+ hits_list = nhmmer(queryfile, seqfile, cpus=args.jobs)
for hits in hits_list:
for hit in hits:
if hit.reported:
@@ -1757,7 +1756,7 @@ if __name__ == "__main__":
def _hmmalign(args: argparse.Namespace) -> int:
try:
with SequenceFile(args.seqfile, args.informat, digital=True) as seqfile:
- sequences: typing.List[DigitalSequence] = list(seqfile) # type: ignore
+ sequences: typing.List[DigitalSequence] = list(seqfile)
except EOFError as err:
print(err, file=sys.stderr)
return 1
diff --git a/pyhmmer/plan7.pyi b/pyhmmer/plan7.pyi
index 2e48f121b8b784b0ec040d80a11794c25e87d411..4393079dbd40f96ce2811807adcc55d70ff20af1 100644
--- a/pyhmmer/plan7.pyi
+++ b/pyhmmer/plan7.pyi
@@ -724,18 +724,18 @@ class Pipeline(object):
def search_hmm(
self,
query: typing.Union[HMM, Profile, OptimizedProfile],
- sequences: typing.Union[DigitalSequenceBlock, SequenceFile],
+ sequences: typing.Union[DigitalSequenceBlock, SequenceFile[DigitalSequence]],
) -> TopHits[typing.Union[HMM, Profile, OptimizedProfile]]: ...
def search_msa(
self,
query: DigitalMSA,
- sequences: typing.Union[DigitalSequenceBlock, SequenceFile],
+ sequences: typing.Union[DigitalSequenceBlock, SequenceFile[DigitalSequence]],
builder: typing.Optional[Builder] = None,
) -> TopHits[DigitalMSA]: ...
def search_seq(
self,
query: DigitalSequence,
- sequences: typing.Union[DigitalSequenceBlock, SequenceFile],
+ sequences: typing.Union[DigitalSequenceBlock, SequenceFile[DigitalSequence]],
builder: typing.Optional[Builder] = None,
) -> TopHits[DigitalSequence]: ...
def scan_seq(