From 4b468e06e43c4ee1b75e8ab506be98b433b6423b Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 17 Jun 2024 14:00:18 +0200
Subject: [PATCH] Document methods of `jaspar16::Record` in `lightmotif-io`
---
lightmotif-io/README.md | 2 +-
lightmotif-io/src/jaspar/mod.rs | 3 +++
lightmotif-io/src/jaspar16/mod.rs | 5 +++++
lightmotif-io/src/transfac/mod.rs | 6 ++++++
4 files changed, 15 insertions(+), 1 deletion(-)
diff --git a/lightmotif-io/README.md b/lightmotif-io/README.md
index 41a8614..b366fb7 100644
--- a/lightmotif-io/README.md
+++ b/lightmotif-io/README.md
@@ -24,7 +24,7 @@ PSSM file formats, including:
- [x] [TRANSFAC](https://en.wikipedia.org/wiki/TRANSFAC)-formatted records,
with associated metadata.
- [x] [JASPAR](https://jaspar.elixir.no/docs/) count matrices
- (in JASPAR 2016 bracketed format) with their record header.
+ (in JASPAR 2016 bracketed format or raw format) with their record header.
- [x] [UniPROBE](http://the_brain.bwh.harvard.edu/uniprobe/index.php)
frequency matrices with their record header.
- [ ] [MEME minimal](https://meme-suite.org/meme/doc/meme-format.html) records
diff --git a/lightmotif-io/src/jaspar/mod.rs b/lightmotif-io/src/jaspar/mod.rs
index 58a1cac..5154cd9 100644
--- a/lightmotif-io/src/jaspar/mod.rs
+++ b/lightmotif-io/src/jaspar/mod.rs
@@ -62,6 +62,7 @@ impl AsRef<CountMatrix<Dna>> for Record {
// ---
+/// An iterative reader for the JASPAR format.
pub struct Reader<B: BufRead> {
buffer: Vec<u8>,
bufread: B,
@@ -69,6 +70,7 @@ pub struct Reader<B: BufRead> {
}
impl<B: BufRead> Reader<B> {
+ /// Create a new `Reader` from a buffered reader.
pub fn new(mut reader: B) -> Self {
let mut buffer = Vec::new();
let start = reader.read_until(b'>', &mut buffer).unwrap_or(1) - 1;
@@ -121,6 +123,7 @@ impl<B: BufRead> Iterator for Reader<B> {
}
}
+/// Read the records from a file in JASPAR format.
pub fn read<B: BufRead>(reader: B) -> self::Reader<B> {
self::Reader::new(reader)
}
diff --git a/lightmotif-io/src/jaspar16/mod.rs b/lightmotif-io/src/jaspar16/mod.rs
index 1eae03b..702f42f 100644
--- a/lightmotif-io/src/jaspar16/mod.rs
+++ b/lightmotif-io/src/jaspar16/mod.rs
@@ -35,14 +35,17 @@ pub struct Record<A: Alphabet> {
}
impl<A: Alphabet> Record<A> {
+ /// Get the identifier of the record.
pub fn id(&self) -> &str {
&self.id
}
+ /// Get the description of the record, if any.
pub fn description(&self) -> Option<&str> {
self.description.as_deref()
}
+ /// Get the count matrix of the record.
pub fn matrix(&self) -> &CountMatrix<A> {
&self.matrix
}
@@ -56,6 +59,7 @@ impl<A: Alphabet> AsRef<CountMatrix<A>> for Record<A> {
// ---
+/// An iterative reader for the JASPAR (2016) format.
pub struct Reader<B: BufRead, A: Alphabet> {
buffer: Vec<u8>,
bufread: B,
@@ -117,6 +121,7 @@ impl<B: BufRead, A: Alphabet> Iterator for Reader<B, A> {
}
}
+/// Read the records from a file in JASPAR (2016) format.
pub fn read<B: BufRead, A: Alphabet>(reader: B) -> self::Reader<B, A> {
self::Reader::new(reader)
}
diff --git a/lightmotif-io/src/transfac/mod.rs b/lightmotif-io/src/transfac/mod.rs
index 8679369..42b7ef7 100644
--- a/lightmotif-io/src/transfac/mod.rs
+++ b/lightmotif-io/src/transfac/mod.rs
@@ -25,26 +25,32 @@ pub struct Record<A: Alphabet> {
}
impl<A: Alphabet> Record<A> {
+ /// The identifier of the record, if any.
pub fn id(&self) -> Option<&str> {
self.id.as_deref()
}
+ /// The accession of the record, if any.
pub fn accession(&self) -> Option<&str> {
self.accession.as_deref()
}
+ /// The name of the record, if any.
pub fn name(&self) -> Option<&str> {
self.name.as_deref()
}
+ /// The description of the record, if any.
pub fn description(&self) -> Option<&str> {
self.description.as_deref()
}
+ /// The raw data found in the matrix.
pub fn data(&self) -> Option<&DenseMatrix<f32, A::K>> {
self.data.as_ref()
}
+ /// The raw data found in the matrix.
pub fn to_counts(&self) -> Option<CountMatrix<A>> {
if let Some(data) = &self.data {
let mut counts = DenseMatrix::<u32, A::K>::new(data.rows());
--
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