From 1e43a1715815be1aee86f8c66e923ee5ccd921ac Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Fri, 30 Aug 2024 21:17:39 +0200
Subject: [PATCH] Add `load` function to `lightmotif-py` to support loading
several `Motif` from a file
---
lightmotif-io/src/jaspar/mod.rs | 6 ++
lightmotif-io/src/jaspar16/mod.rs | 5 ++
lightmotif-io/src/uniprobe/mod.rs | 5 ++
lightmotif-py/Cargo.toml | 3 +
lightmotif-py/lightmotif/io.rs | 108 ++++++++++++++++++++++++++++++
lightmotif-py/lightmotif/lib.rs | 43 +++++++++++-
6 files changed, 168 insertions(+), 2 deletions(-)
create mode 100644 lightmotif-py/lightmotif/io.rs
diff --git a/lightmotif-io/src/jaspar/mod.rs b/lightmotif-io/src/jaspar/mod.rs
index 4c69a67..98168f7 100644
--- a/lightmotif-io/src/jaspar/mod.rs
+++ b/lightmotif-io/src/jaspar/mod.rs
@@ -60,6 +60,12 @@ impl AsRef<CountMatrix<Dna>> for Record {
}
}
+impl From<Record> for CountMatrix<Dna> {
+ fn from(value: Record) -> Self {
+ value.matrix
+ }
+}
+
// ---
/// An iterative reader for the JASPAR format.
diff --git a/lightmotif-io/src/jaspar16/mod.rs b/lightmotif-io/src/jaspar16/mod.rs
index e1ec1d5..d302ab7 100644
--- a/lightmotif-io/src/jaspar16/mod.rs
+++ b/lightmotif-io/src/jaspar16/mod.rs
@@ -49,6 +49,11 @@ impl<A: Alphabet> Record<A> {
pub fn matrix(&self) -> &CountMatrix<A> {
&self.matrix
}
+
+ /// Take the count matrix of the record.
+ pub fn into_matrix(self) -> CountMatrix<A> {
+ self.matrix
+ }
}
impl<A: Alphabet> AsRef<CountMatrix<A>> for Record<A> {
diff --git a/lightmotif-io/src/uniprobe/mod.rs b/lightmotif-io/src/uniprobe/mod.rs
index 8254626..7a0797c 100644
--- a/lightmotif-io/src/uniprobe/mod.rs
+++ b/lightmotif-io/src/uniprobe/mod.rs
@@ -39,6 +39,11 @@ impl<A: Alphabet> Record<A> {
pub fn matrix(&self) -> &FrequencyMatrix<A> {
&self.matrix
}
+
+ /// Take the frequency matrix of the record.
+ pub fn into_matrix(self) -> FrequencyMatrix<A> {
+ self.matrix
+ }
}
impl<A: Alphabet> AsRef<FrequencyMatrix<A>> for Record<A> {
diff --git a/lightmotif-py/Cargo.toml b/lightmotif-py/Cargo.toml
index c18617b..59d9bf3 100644
--- a/lightmotif-py/Cargo.toml
+++ b/lightmotif-py/Cargo.toml
@@ -19,6 +19,9 @@ doctest = false
[dependencies.lightmotif]
path = "../lightmotif"
version = "0.8.0"
+[dependencies.lightmotif-io]
+path = "../lightmotif-io"
+version = "0.8.0"
[dependencies.lightmotif-tfmpvalue]
optional = true
path = "../lightmotif-tfmpvalue"
diff --git a/lightmotif-py/lightmotif/io.rs b/lightmotif-py/lightmotif/io.rs
new file mode 100644
index 0000000..8976169
--- /dev/null
+++ b/lightmotif-py/lightmotif/io.rs
@@ -0,0 +1,108 @@
+use lightmotif::abc::Alphabet;
+use lightmotif::abc::Dna;
+use lightmotif::abc::Protein;
+use lightmotif_io::error::Error;
+
+use pyo3::exceptions::PyValueError;
+use pyo3::prelude::*;
+
+use super::CountMatrixData;
+use super::Motif;
+use super::ScoringMatrixData;
+use super::WeightMatrixData;
+
+fn convert_jaspar(record: Result<lightmotif_io::jaspar::Record, Error>) -> PyResult<Motif> {
+ let record = record.unwrap();
+ let counts = record.into();
+ Python::with_gil(|py| Motif::from_counts(py, counts))
+}
+
+fn convert_jaspar16<A>(record: Result<lightmotif_io::jaspar16::Record<A>, Error>) -> PyResult<Motif>
+where
+ A: Alphabet,
+ CountMatrixData: From<lightmotif::pwm::CountMatrix<A>>,
+ WeightMatrixData: From<lightmotif::pwm::WeightMatrix<A>>,
+ ScoringMatrixData: From<lightmotif::pwm::ScoringMatrix<A>>,
+{
+ let record = record.unwrap();
+ let counts = record.into_matrix();
+ Python::with_gil(|py| Motif::from_counts(py, counts))
+}
+
+fn convert_transfac<A>(record: Result<lightmotif_io::transfac::Record<A>, Error>) -> PyResult<Motif>
+where
+ A: Alphabet,
+ CountMatrixData: From<lightmotif::pwm::CountMatrix<A>>,
+ WeightMatrixData: From<lightmotif::pwm::WeightMatrix<A>>,
+ ScoringMatrixData: From<lightmotif::pwm::ScoringMatrix<A>>,
+{
+ let record = record.unwrap();
+ let counts = record
+ .to_counts()
+ .ok_or_else(|| PyValueError::new_err("invalid count matrix"))?;
+ Python::with_gil(|py| Motif::from_counts(py, counts))
+}
+
+fn convert_uniprobe<A>(record: Result<lightmotif_io::uniprobe::Record<A>, Error>) -> PyResult<Motif>
+where
+ A: Alphabet,
+ WeightMatrixData: From<lightmotif::pwm::WeightMatrix<A>>,
+ ScoringMatrixData: From<lightmotif::pwm::ScoringMatrix<A>>,
+{
+ let record = record.unwrap();
+ let freqs = record.into_matrix();
+ let weights = freqs.to_weight(None);
+ Python::with_gil(|py| Motif::from_weights(py, weights))
+}
+
+#[pyclass(module = "lightmotif.lib")]
+pub struct Loader {
+ reader: Box<dyn Iterator<Item = PyResult<Motif>> + Send>,
+}
+
+#[pymethods]
+impl Loader {
+ fn __iter__(slf: PyRef<Self>) -> PyRef<Self> {
+ slf
+ }
+
+ fn __next__(mut slf: PyRefMut<Self>) -> Option<PyResult<Motif>> {
+ slf.reader.next()
+ }
+}
+
+#[pyfunction]
+#[pyo3(signature = (path, format="jaspar", protein=false))]
+pub fn load(path: &str, format: &str, protein: bool) -> PyResult<Loader> {
+ let file = std::fs::File::open(path)
+ .map(std::io::BufReader::new)
+ .unwrap();
+ let reader: Box<dyn Iterator<Item = PyResult<Motif>> + Send> = match format {
+ "jaspar" if protein => {
+ return Err(PyValueError::new_err(
+ "cannot read protein motifs from JASPAR format",
+ ))
+ }
+ "jaspar16" if protein => Box::new(
+ lightmotif_io::jaspar16::read::<_, Protein>(file).map(convert_jaspar16::<Protein>),
+ ),
+ "transfac" if protein => Box::new(
+ lightmotif_io::transfac::read::<_, Protein>(file).map(convert_transfac::<Protein>),
+ ),
+ "uniprobe" if protein => Box::new(
+ lightmotif_io::uniprobe::read::<_, Protein>(file).map(convert_uniprobe::<Protein>),
+ ),
+ "jaspar" => Box::new(lightmotif_io::jaspar::read(file).map(convert_jaspar)),
+ "jaspar16" => {
+ Box::new(lightmotif_io::jaspar16::read::<_, Dna>(file).map(convert_jaspar16::<Dna>))
+ }
+ "transfac" => {
+ Box::new(lightmotif_io::transfac::read::<_, Dna>(file).map(convert_transfac::<Dna>))
+ }
+ "uniprobe" => {
+ Box::new(lightmotif_io::uniprobe::read::<_, Dna>(file).map(convert_uniprobe::<Dna>))
+ }
+ _ => return Err(PyValueError::new_err(format!("invalid format: {}", format))),
+ };
+ Ok(Loader { reader })
+}
diff --git a/lightmotif-py/lightmotif/lib.rs b/lightmotif-py/lightmotif/lib.rs
index 2ac43b1..79bc65f 100644
--- a/lightmotif-py/lightmotif/lib.rs
+++ b/lightmotif-py/lightmotif/lib.rs
@@ -34,6 +34,10 @@ use pyo3::types::PyDict;
use pyo3::types::PyList;
use pyo3::types::PyString;
+mod io;
+
+// --- Macros ------------------------------------------------------------------
+
macro_rules! impl_matrix_methods {
($datatype:ident) => {
impl $datatype {
@@ -1040,13 +1044,45 @@ impl From<lightmotif::scores::StripedScores<f32, C>> for StripedScores {
#[derive(Debug)]
pub struct Motif {
#[pyo3(get)]
- counts: Py<CountMatrix>,
+ counts: Option<Py<CountMatrix>>,
#[pyo3(get)]
pwm: Py<WeightMatrix>,
#[pyo3(get)]
pssm: Py<ScoringMatrix>,
}
+impl Motif {
+ fn from_counts<A>(py: Python, counts: lightmotif::pwm::CountMatrix<A>) -> PyResult<Self>
+ where
+ A: Alphabet,
+ CountMatrixData: From<lightmotif::pwm::CountMatrix<A>>,
+ WeightMatrixData: From<lightmotif::pwm::WeightMatrix<A>>,
+ ScoringMatrixData: From<lightmotif::pwm::ScoringMatrix<A>>,
+ {
+ let weights = counts.to_freq(0.0).to_weight(None);
+ let scoring = weights.to_scoring();
+ Ok(Motif {
+ counts: Some(Py::new(py, CountMatrix::new(counts))?),
+ pwm: Py::new(py, WeightMatrix::new(weights))?,
+ pssm: Py::new(py, ScoringMatrix::new(scoring))?,
+ })
+ }
+
+ fn from_weights<A>(py: Python, weights: lightmotif::pwm::WeightMatrix<A>) -> PyResult<Self>
+ where
+ A: Alphabet,
+ WeightMatrixData: From<lightmotif::pwm::WeightMatrix<A>>,
+ ScoringMatrixData: From<lightmotif::pwm::ScoringMatrix<A>>,
+ {
+ let scoring = weights.to_scoring();
+ Ok(Motif {
+ counts: None,
+ pwm: Py::new(py, WeightMatrix::new(weights))?,
+ pssm: Py::new(py, ScoringMatrix::new(scoring))?,
+ })
+ }
+}
+
// --- Scanner -----------------------------------------------------------------
#[derive(Debug)]
@@ -1139,7 +1175,7 @@ pub fn create(sequences: Bound<PyAny>, protein: bool) -> PyResult<Motif> {
let scoring = weights.to_scoring();
Ok(Motif {
- counts: Py::new(py, CountMatrix::new(data))?,
+ counts: Some(Py::new(py, CountMatrix::new(data))?),
pwm: Py::new(py, WeightMatrix::new(weights))?,
pssm: Py::new(py, ScoringMatrix::new(scoring))?,
})
@@ -1251,9 +1287,12 @@ pub fn init<'py>(_py: Python<'py>, m: &Bound<PyModule>) -> PyResult<()> {
m.add_class::<Scanner>()?;
m.add_class::<Hit>()?;
+ m.add_class::<io::Loader>()?;
+
m.add_function(wrap_pyfunction!(create, m)?)?;
m.add_function(wrap_pyfunction!(scan, m)?)?;
m.add_function(wrap_pyfunction!(stripe, m)?)?;
+ m.add_function(wrap_pyfunction!(io::load, m)?)?;
Ok(())
}
--
GitLab