diff --git a/lightmotif-py/lightmotif/lib.pyi b/lightmotif-py/lightmotif/lib.pyi
index 059b291bf90129490902784b0cefb785e1d9c787..4b12555e8648badf88bd5c10b31f69796c49932e 100644
--- a/lightmotif-py/lightmotif/lib.pyi
+++ b/lightmotif-py/lightmotif/lib.pyi
@@ -15,7 +15,7 @@ AVX2_SUPPORTED: bool
FORMAT = Literal["jaspar", "jaspar16", "uniprobe", "transfac"]
class EncodedSequence:
- def __init__(self, sequence: str, protein: bool = False) -> None: ...
+ def __init__(self, sequence: str, *, protein: bool = False) -> None: ...
def __str__(self) -> str: ...
def __len__(self) -> int: ...
def __copy__(self) -> EncodedSequence: ...
@@ -34,7 +34,7 @@ class StripedSequence:
class CountMatrix:
def __init__(
- self, values: Dict[str, Iterable[int]], protein: bool = False
+ self, values: Dict[str, Iterable[int]], *, protein: bool = False
) -> None: ...
def __eq__(self, other: object) -> bool: ...
def __len__(self) -> int: ...
@@ -57,7 +57,11 @@ class WeightMatrix:
class ScoringMatrix:
def __init__(
- self, values: Dict[str, Iterable[float]], protein: bool = False
+ self,
+ values: Dict[str, Iterable[float]],
+ background: Optional[Dict[str, float]] = None,
+ *,
+ protein: bool = False,
) -> None: ...
def __len__(self) -> int: ...
def __eq__(self, other: object) -> bool: ...
@@ -125,16 +129,24 @@ class Hit:
M = typing.TypeVar("M", bound=Motif)
class Loader(Generic[M], Iterator[M]):
+ def __init__(
+ self,
+ file: Union[BinaryIO, PathLike[str]],
+ format: Literal["jaspar16"],
+ *,
+ protein: bool = False,
+ ) -> None: ...
def __iter__(self) -> Loader[M]: ...
def __next__(self) -> M: ...
def create(
- sequences: Iterable[str], protein: bool = False, name: Optional[str] = None
+ sequences: Iterable[str], *, protein: bool = False, name: Optional[str] = None
) -> Motif: ...
-def stripe(sequence: str, protein: bool = False) -> StripedSequence: ...
+def stripe(sequence: str, *, protein: bool = False) -> StripedSequence: ...
def scan(
pssm: ScoringMatrix,
sequence: StripedSequence,
+ *,
threshold: float = 0.0,
block_size: int = 256,
) -> Scanner: ...
@@ -143,33 +155,33 @@ def load(
file: Union[BinaryIO, PathLike[str]],
format: Literal["jaspar"],
*,
- protein: bool = False
+ protein: bool = False,
) -> Loader[JasparMotif]: ...
@typing.overload
def load(
file: Union[BinaryIO, PathLike[str]],
format: Literal["jaspar16"],
*,
- protein: bool = False
+ protein: bool = False,
) -> Loader[JasparMotif]: ...
@typing.overload
def load(
file: Union[BinaryIO, PathLike[str]],
format: Literal["uniprobe"],
*,
- protein: bool = False
+ protein: bool = False,
) -> Loader[UniprobeMotif]: ...
@typing.overload
def load(
file: Union[BinaryIO, PathLike[str]],
format: Literal["transfac"],
*,
- protein: bool = False
+ protein: bool = False,
) -> Loader[TransfacMotif]: ...
@typing.overload
def load(
file: Union[BinaryIO, PathLike[str]],
format: FORMAT = "jaspar",
*,
- protein: bool = False
+ protein: bool = False,
) -> Loader[Motif]: ...
diff --git a/lightmotif-py/lightmotif/lib.rs b/lightmotif-py/lightmotif/lib.rs
index bef9b876d82dc712f122d7db301d37bfe0c9bb11..4c867e0368e6ef6d80e7c9d211154114858a6b2b 100644
--- a/lightmotif-py/lightmotif/lib.rs
+++ b/lightmotif-py/lightmotif/lib.rs
@@ -434,7 +434,7 @@ impl CountMatrix {
/// Create a new count matrix.
#[new]
#[allow(unused_variables)]
- #[pyo3(signature = (values, protein = false))]
+ #[pyo3(signature = (values, *, protein = false))]
pub fn __init__<'py>(
values: Bound<'py, PyDict>,
protein: bool,
@@ -746,50 +746,63 @@ impl ScoringMatrix {
impl ScoringMatrix {
/// Create a new scoring matrix.
#[new]
- #[pyo3(signature = (alphabet, values, background = None))]
+ #[pyo3(signature = (values, background = None, *, protein = false))]
#[allow(unused)]
pub fn __init__<'py>(
- alphabet: Bound<'py, PyString>,
values: Bound<'py, PyDict>,
background: Option<PyObject>,
+ protein: bool,
) -> PyResult<PyClassInitializer<Self>> {
- // extract the background from the method argument
- let bg = Python::with_gil(|py| {
- if let Some(obj) = background {
- if let Ok(d) = obj.extract::<Bound<PyDict>>(py) {
- let p = dict_to_alphabet_array::<Dna>(d)?;
- lightmotif::abc::Background::new(p)
- .map_err(|_| PyValueError::new_err("Invalid background frequencies"))
- } else {
- Err(PyTypeError::new_err("Invalid type for pseudocount"))
- }
- } else {
- Ok(lightmotif::abc::Background::uniform())
- }
- })?;
-
- // build data
- let mut data: Option<DenseMatrix<f32, <Dna as Alphabet>::K>> = None;
- for s in Dna::symbols() {
- let key = String::from(s.as_char());
- if let Some(res) = values.get_item(&key)? {
- let column = res.downcast::<PyList>()?;
- if data.is_none() {
- data = Some(DenseMatrix::new(column.len()));
- }
- let matrix = data.as_mut().unwrap();
- if matrix.rows() != column.len() {
- return Err(PyValueError::new_err("Invalid number of rows"));
+ macro_rules! run {
+ ($alphabet:ty) => {{
+ // extract the background from the method argument
+ let bg = Python::with_gil(|py| {
+ if let Some(obj) = background {
+ if let Ok(d) = obj.extract::<Bound<PyDict>>(py) {
+ let p = dict_to_alphabet_array::<$alphabet>(d)?;
+ lightmotif::abc::Background::<$alphabet>::new(p).map_err(|_| {
+ PyValueError::new_err("Invalid background frequencies")
+ })
+ } else {
+ Err(PyTypeError::new_err("Invalid type for pseudocount"))
+ }
+ } else {
+ Ok(lightmotif::abc::Background::uniform())
+ }
+ })?;
+ // build data
+ let mut data: Option<DenseMatrix<f32, <$alphabet as Alphabet>::K>> = None;
+ for s in <$alphabet as Alphabet>::symbols() {
+ let key = String::from(s.as_char());
+ if let Some(res) = values.get_item(&key)? {
+ let column = res.downcast::<PyList>()?;
+ if data.is_none() {
+ data = Some(DenseMatrix::new(column.len()));
+ }
+ let matrix = data.as_mut().unwrap();
+ if matrix.rows() != column.len() {
+ return Err(PyValueError::new_err("Invalid number of rows"));
+ }
+ for (i, x) in column.iter().enumerate() {
+ matrix[i][s.as_index()] = x.extract::<f32>()?;
+ }
+ }
}
- for (i, x) in column.iter().enumerate() {
- matrix[i][s.as_index()] = x.extract::<f32>()?;
+ // create matrix
+ match data {
+ None => Err(PyValueError::new_err("Invalid count matrix")),
+ Some(matrix) => Ok(Self::new(lightmotif::ScoringMatrix::<$alphabet>::new(
+ bg, matrix,
+ ))
+ .into()),
}
- }
+ }};
}
- match data {
- None => Err(PyValueError::new_err("Invalid count matrix")),
- Some(matrix) => Ok(Self::new(lightmotif::ScoringMatrix::<Dna>::new(bg, matrix)).into()),
+ if protein {
+ run!(Protein)
+ } else {
+ run!(Dna)
}
}
@@ -1272,7 +1285,7 @@ impl From<lightmotif::scan::Hit> for Hit {
/// or when the sequence lengths are not consistent.
///
#[pyfunction]
-#[pyo3(signature = (sequences, protein = false, name = None))]
+#[pyo3(signature = (sequences, *, protein = false, name = None))]
pub fn create(sequences: Bound<PyAny>, protein: bool, name: Option<String>) -> PyResult<Motif> {
let py = sequences.py();
macro_rules! run {
@@ -1323,7 +1336,7 @@ pub fn create(sequences: Bound<PyAny>, protein: bool, name: Option<String>) -> P
/// `ValueError`: When the sequences contains an invalid character.
///
#[pyfunction]
-#[pyo3(signature = (sequence, protein=false))]
+#[pyo3(signature = (sequence, *, protein=false))]
pub fn stripe(sequence: Bound<PyString>, protein: bool) -> PyResult<StripedSequence> {
let py = sequence.py();
let encoded = EncodedSequence::__init__(sequence, protein).and_then(|e| Py::new(py, e))?;
@@ -1359,7 +1372,7 @@ pub fn stripe(sequence: Bound<PyString>, protein: bool) -> PyResult<StripedSeque
/// implementation requirements.
///
#[pyfunction]
-#[pyo3(signature = (pssm, sequence, threshold = 0.0, block_size = 256))]
+#[pyo3(signature = (pssm, sequence, *, threshold = 0.0, block_size = 256))]
pub fn scan<'py>(
pssm: Bound<'py, ScoringMatrix>,
sequence: Bound<'py, StripedSequence>,