From f6950e9b9ad2c23d29c6a0f93e1da98a20ceb6d3 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 2 Sep 2024 13:08:55 +0200
Subject: [PATCH] Implement `Scanner.__init__` and fix type annotations in
Python package
---
lightmotif-py/lightmotif/lib.pyi | 11 +++++
lightmotif-py/lightmotif/lib.rs | 77 +++++++++++++++++++-------------
2 files changed, 57 insertions(+), 31 deletions(-)
diff --git a/lightmotif-py/lightmotif/lib.pyi b/lightmotif-py/lightmotif/lib.pyi
index 41cc93c..91cd2e3 100644
--- a/lightmotif-py/lightmotif/lib.pyi
+++ b/lightmotif-py/lightmotif/lib.pyi
@@ -84,12 +84,23 @@ class TransfacMotif(Motif):
class JasparMotif(Motif):
@property
def counts(self) -> CountMatrix: ...
+ @property
+ def name(self) -> str: ...
+ @property
+ def description(self) -> Optional[str]: ...
class UniprobeMotif(Motif):
@property
def counts(self) -> None: ...
class Scanner(Iterator[Hit]):
+ def __init__(
+ self,
+ pssm: ScoringMatrix,
+ sequence: StripedSequence,
+ threshold: float = 0.0,
+ block_size: int = 256,
+ ) -> None: ...
def __iter__(self) -> Scanner: ...
def __next__(self) -> Hit: ...
diff --git a/lightmotif-py/lightmotif/lib.rs b/lightmotif-py/lightmotif/lib.rs
index 6eedc89..98b4d19 100644
--- a/lightmotif-py/lightmotif/lib.rs
+++ b/lightmotif-py/lightmotif/lib.rs
@@ -312,7 +312,10 @@ impl From<StripedSequenceData> for StripedSequence {
let cols = data.columns();
let rows = data.rows();
let shape = [cols as Py_ssize_t, rows as Py_ssize_t];
- let strides = [1, data.stride() as Py_ssize_t];
+ let strides = [
+ std::mem::size_of::<u8>() as Py_ssize_t,
+ (std::mem::size_of::<u8>() * data.stride()) as Py_ssize_t,
+ ];
Self {
data,
shape,
@@ -1107,6 +1110,44 @@ pub struct Scanner {
#[pymethods]
impl Scanner {
+ #[new]
+ #[pyo3(signature = (pssm, sequence, threshold = 0.0, block_size = 256))]
+ fn __init__<'py>(
+ pssm: Bound<'py, ScoringMatrix>,
+ sequence: Bound<'py, StripedSequence>,
+ threshold: f32,
+ block_size: usize,
+ ) -> PyResult<PyClassInitializer<Self>> {
+ match (
+ &pssm.try_borrow()?.data,
+ &mut sequence.try_borrow_mut()?.data,
+ ) {
+ (ScoringMatrixData::Dna(p), StripedSequenceData::Dna(s)) => {
+ s.configure(&p);
+ // transmute (!!!!!) the scanner so that its lifetime is 'static
+ // (i.e. the reference to the PSSM and sequence never expire),
+ // which is possible because we are building a self-referential
+ // struct and self.scanner.next() will only be called with
+ // the GIL held...
+ let scanner = unsafe {
+ let mut scanner = lightmotif::scan::Scanner::<Dna, _, _, C>::new(p, s);
+ scanner.threshold(threshold);
+ scanner.block_size(block_size);
+ std::mem::transmute(scanner)
+ };
+ Ok(PyClassInitializer::from(Scanner {
+ data: scanner,
+ pssm: pssm.unbind(),
+ sequence: sequence.unbind(),
+ }))
+ }
+ (ScoringMatrixData::Protein(_), StripedSequenceData::Protein(_)) => {
+ Err(PyValueError::new_err("protein scanner is not supported"))
+ }
+ (_, _) => Err(PyValueError::new_err("alphabet mismatch")),
+ }
+ }
+
fn __iter__(slf: PyRef<Self>) -> PyRef<Self> {
slf
}
@@ -1216,36 +1257,10 @@ pub fn scan<'py>(
block_size: usize,
) -> PyResult<Bound<'py, Scanner>> {
let py = pssm.py();
- match (
- &pssm.try_borrow()?.data,
- &mut sequence.try_borrow_mut()?.data,
- ) {
- (ScoringMatrixData::Dna(p), StripedSequenceData::Dna(s)) => {
- s.configure(&p);
- // transmute (!!!!!) the scanner so that its lifetime is 'static
- // (i.e. the reference to the PSSM and sequence never expire),
- // which is possible because we are building a self-referential
- // struct
- let scanner = unsafe {
- let mut scanner = lightmotif::scan::Scanner::<Dna, _, _, C>::new(p, s);
- scanner.threshold(threshold);
- scanner.block_size(block_size);
- std::mem::transmute(scanner)
- };
- Bound::new(
- py,
- Scanner {
- data: scanner,
- pssm: pssm.unbind(),
- sequence: sequence.unbind(),
- },
- )
- }
- (ScoringMatrixData::Protein(_), StripedSequenceData::Protein(_)) => {
- Err(PyValueError::new_err("protein scanner is not supported"))
- }
- (_, _) => Err(PyValueError::new_err("alphabet mismatch")),
- }
+ Bound::new(
+ py,
+ Scanner::__init__(pssm, sequence, threshold, block_size)?,
+ )
}
// --- Module ------------------------------------------------------------------
--
GitLab