From a6f239367101ec5cd276c3018c3d27952d995359 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 2 Sep 2024 00:37:45 +0200
Subject: [PATCH] Add type annotations for `lightmotif.lib` Python module
---
lightmotif-py/lightmotif/io.rs | 3 +
lightmotif-py/lightmotif/lib.pyi | 152 ++++++++++++++++++++++++++++++
lightmotif-py/lightmotif/lib.rs | 5 +-
lightmotif-py/lightmotif/py.typed | 0
setup.cfg | 2 +-
5 files changed, 158 insertions(+), 4 deletions(-)
create mode 100644 lightmotif-py/lightmotif/lib.pyi
create mode 100644 lightmotif-py/lightmotif/py.typed
diff --git a/lightmotif-py/lightmotif/io.rs b/lightmotif-py/lightmotif/io.rs
index ea1432c..6d18d48 100644
--- a/lightmotif-py/lightmotif/io.rs
+++ b/lightmotif-py/lightmotif/io.rs
@@ -100,8 +100,11 @@ impl UniprobeMotif {
#[pyclass(module = "lightmotif.lib", extends = Motif)]
pub struct TransfacMotif {
+ #[pyo3(get)]
id: Option<String>,
+ #[pyo3(get)]
accession: Option<String>,
+ #[pyo3(get)]
description: Option<String>,
}
diff --git a/lightmotif-py/lightmotif/lib.pyi b/lightmotif-py/lightmotif/lib.pyi
new file mode 100644
index 0000000..41cc93c
--- /dev/null
+++ b/lightmotif-py/lightmotif/lib.pyi
@@ -0,0 +1,152 @@
+import typing
+from typing import Dict, List, Iterable, Union, Optional, BinaryIO, Iterator, Generic
+from os import PathLike
+
+try:
+ from typing import Literal
+except ImportError:
+ from typing_extensions import Literal # type: ignore
+
+__version__: str
+__author__: str
+
+AVX2_SUPPORTED: bool
+
+FORMAT = Literal["jaspar", "jaspar16", "uniprobe", "transfac"]
+
+class EncodedSequence:
+ def __init__(self, sequence: str, protein: bool = False) -> None: ...
+ def __str__(self) -> str: ...
+ def __len__(self) -> int: ...
+ def __copy__(self) -> EncodedSequence: ...
+ def __buffer__(self, flags: int) -> memoryview: ...
+ def copy(self) -> EncodedSequence: ...
+ def stripe(self) -> StripedSequence: ...
+
+class StripedSequence:
+ def __copy__(self) -> StripedSequence: ...
+ def __buffer__(self, flags: int) -> memoryview: ...
+ def copy(self) -> StripedSequence: ...
+
+class CountMatrix:
+ def __init__(
+ self, values: Dict[str, Iterable[int]], protein: bool = False
+ ) -> None: ...
+ def __eq__(self, other: object) -> bool: ...
+ def __len__(self) -> int: ...
+ def __getitem__(self, index: int) -> List[int]: ...
+ def normalize(
+ self, pseudocount: Union[None, float, Dict[str, float]] = None
+ ) -> WeightMatrix: ...
+
+class WeightMatrix:
+ def __eq__(self, other: object) -> bool: ...
+ def __len__(self) -> int: ...
+ def __getitem__(self, index: int) -> List[int]: ...
+ def log_odds(
+ self, background: Union[None, Dict[str, float]] = None, base: float = 2.0
+ ) -> ScoringMatrix: ...
+
+class ScoringMatrix:
+ def __init__(
+ self, values: Dict[str, Iterable[float]], protein: bool = False
+ ) -> None: ...
+ def __len__(self) -> int: ...
+ def __eq__(self, other: object) -> bool: ...
+ def __buffer__(self, flags: int) -> memoryview: ...
+ def calculate(self, sequence: StripedSequence) -> StripedScores: ...
+ def pvalue(self, score: float) -> float: ...
+ def score(self, pvalue: float) -> float: ...
+ def reverse_complement(self) -> ScoringMatrix: ...
+
+class StripedScores:
+ def __len__(self) -> int: ...
+ def __getitem__(self, index: int) -> float: ...
+ def __buffer__(self, flags: int) -> memoryview: ...
+ def threshold(self, threshold: float) -> List[int]: ...
+ def max(self) -> Optional[float]: ...
+ def argmax(self) -> Optional[int]: ...
+
+class Motif:
+ @property
+ def counts(self) -> Optional[CountMatrix]: ...
+ @property
+ def pwm(self) -> WeightMatrix: ...
+ @property
+ def pssm(self) -> ScoringMatrix: ...
+ @property
+ def name(self) -> Optional[str]: ...
+
+class TransfacMotif(Motif):
+ @property
+ def counts(self) -> CountMatrix: ...
+
+class JasparMotif(Motif):
+ @property
+ def counts(self) -> CountMatrix: ...
+
+class UniprobeMotif(Motif):
+ @property
+ def counts(self) -> None: ...
+
+class Scanner(Iterator[Hit]):
+ def __iter__(self) -> Scanner: ...
+ def __next__(self) -> Hit: ...
+
+class Hit:
+ @property
+ def position(self) -> int: ...
+ @property
+ def score(self) -> float: ...
+
+M = typing.TypeVar("M", bound=Motif)
+
+class Loader(Generic[M], Iterator[M]):
+ def __iter__(self) -> Loader[M]: ...
+ def __next__(self) -> M: ...
+
+def create(
+ sequences: Iterable[str], protein: bool = False, name: Optional[str] = None
+) -> Motif: ...
+def stripe(sequence: str, protein: bool = False) -> StripedSequence: ...
+def scan(
+ pssm: ScoringMatrix,
+ sequence: StripedSequence,
+ threshold: float = 0.0,
+ block_size: int = 256,
+) -> Scanner: ...
+@typing.overload
+def load(
+ file: Union[BinaryIO, PathLike[str]],
+ format: Literal["jaspar"],
+ *,
+ protein: bool = False
+) -> Loader[JasparMotif]: ...
+@typing.overload
+def load(
+ file: Union[BinaryIO, PathLike[str]],
+ format: Literal["jaspar16"],
+ *,
+ protein: bool = False
+) -> Loader[JasparMotif]: ...
+@typing.overload
+def load(
+ file: Union[BinaryIO, PathLike[str]],
+ format: Literal["uniprobe"],
+ *,
+ protein: bool = False
+) -> Loader[UniprobeMotif]: ...
+@typing.overload
+def load(
+ file: Union[BinaryIO, PathLike[str]],
+ format: Literal["transfac"],
+ *,
+ protein: bool = False
+) -> Loader[TransfacMotif]: ...
+@typing.overload
+def load(
+ file: Union[BinaryIO, PathLike[str]],
+ format: FORMAT = "jaspar",
+ *,
+ protein: bool = False
+) -> Loader[Motif]: ...
diff --git a/lightmotif-py/lightmotif/lib.rs b/lightmotif-py/lightmotif/lib.rs
index 310aae7..36918f8 100644
--- a/lightmotif-py/lightmotif/lib.rs
+++ b/lightmotif-py/lightmotif/lib.rs
@@ -1202,10 +1202,9 @@ pub fn create(sequences: Bound<PyAny>, protein: bool, name: Option<String>) -> P
/// Encode and stripe a text sequence.
#[pyfunction]
#[pyo3(signature = (sequence, protein=false))]
-pub fn stripe(sequence: Bound<PyAny>, protein: bool) -> PyResult<StripedSequence> {
+pub fn stripe(sequence: Bound<PyString>, protein: bool) -> PyResult<StripedSequence> {
let py = sequence.py();
- let s = sequence.extract::<Bound<PyString>>()?;
- let encoded = EncodedSequence::__init__(s, protein).and_then(|e| Py::new(py, e))?;
+ let encoded = EncodedSequence::__init__(sequence, protein).and_then(|e| Py::new(py, e))?;
let striped = encoded.borrow(py).stripe();
striped
}
diff --git a/lightmotif-py/lightmotif/py.typed b/lightmotif-py/lightmotif/py.typed
new file mode 100644
index 0000000..e69de29
diff --git a/setup.cfg b/setup.cfg
index 946c470..34bcb00 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -32,7 +32,7 @@ classifiers =
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Medical Science Apps.
Topic :: Software Development :: Libraries :: Python Modules
- # Typing :: Typed
+ Typing :: Typed
project_urls =
Bug Tracker = https://github.com/althonos/lightmotif/issues
Changelog = https://github.com/althonos/lightmotif/blob/master/CHANGELOG.md
--
GitLab