From 41a6d1f729a217e05913b0de52fce605f30bda99 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Fri, 21 Jun 2024 16:52:48 +0200
Subject: [PATCH] Add tests to ensure `Maximum::argmax` works as expected for
all implementations
---
lightmotif/src/pli/mod.rs | 4 +-
lightmotif/tests/argmax.rs | 142 +++++++++++++++++++++++++++++++++++++
2 files changed, 145 insertions(+), 1 deletion(-)
create mode 100644 lightmotif/tests/argmax.rs
diff --git a/lightmotif/src/pli/mod.rs b/lightmotif/src/pli/mod.rs
index 1a5f57f..80a053b 100644
--- a/lightmotif/src/pli/mod.rs
+++ b/lightmotif/src/pli/mod.rs
@@ -3,6 +3,8 @@
use std::ops::AddAssign;
use std::ops::Range;
+use generic_array::ArrayLength;
+
use crate::abc::Alphabet;
use crate::abc::Dna;
use crate::abc::Protein;
@@ -361,7 +363,7 @@ where
impl<A, C> Maximum<f32, C> for Pipeline<A, Sse2>
where
A: Alphabet,
- C: StrictlyPositive + MultipleOf<U16>,
+ C: StrictlyPositive + MultipleOf<U16> + ArrayLength,
{
#[inline]
fn argmax(&self, scores: &StripedScores<f32, C>) -> Option<MatrixCoordinates> {
diff --git a/lightmotif/tests/argmax.rs b/lightmotif/tests/argmax.rs
new file mode 100644
index 0000000..fdab04e
--- /dev/null
+++ b/lightmotif/tests/argmax.rs
@@ -0,0 +1,142 @@
+extern crate lightmotif;
+
+use lightmotif::abc::Background;
+use lightmotif::abc::Dna;
+use lightmotif::num::StrictlyPositive;
+use lightmotif::num::U1;
+use lightmotif::num::U16;
+use lightmotif::num::U32;
+use lightmotif::pli::Maximum;
+use lightmotif::pli::Pipeline;
+use lightmotif::pli::Score;
+use lightmotif::pli::Stripe;
+use lightmotif::pwm::CountMatrix;
+use lightmotif::scan::Scanner;
+use lightmotif::scores::StripedScores;
+use lightmotif::seq::EncodedSequence;
+
+const SEQUENCE: &str = include_str!("../benches/ecoli.txt");
+const PATTERNS: &[&str] = &["GTTGACCTTATCAAC", "GTTGATCCAGTCAAC"];
+const N: usize = SEQUENCE.len() / 10;
+
+fn test_argmax_f32<C: StrictlyPositive, P: Maximum<f32, C>>(pli: &P) {
+ let generic = Pipeline::generic();
+
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+ let mut striped = generic.stripe(encoded);
+
+ let bg = Background::<Dna>::uniform();
+ let cm = PATTERNS
+ .iter()
+ .map(EncodedSequence::encode)
+ .map(Result::unwrap)
+ .collect::<Result<CountMatrix<Dna>, _>>()
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+
+ striped.configure(&pssm);
+ let scores: StripedScores<f32, C> = generic.score(pssm, striped);
+
+ let best = scores
+ .unstripe()
+ .iter()
+ .cloned()
+ .enumerate()
+ .max_by(|x, y| x.1.partial_cmp(&y.1).unwrap())
+ .unwrap();
+ let m = pli.argmax(&scores).unwrap();
+ assert_eq!(scores.offset(m), best.0);
+ assert_eq!(scores.matrix()[m], best.1);
+}
+
+mod generic {
+ use super::*;
+
+ #[test]
+ fn argmax_f32() {
+ let pli = Pipeline::<Dna, _>::generic();
+ super::test_argmax_f32::<U1, _>(&pli);
+ super::test_argmax_f32::<U16, _>(&pli);
+ super::test_argmax_f32::<U32, _>(&pli);
+ }
+}
+
+mod dispatch {
+ use super::*;
+
+ #[test]
+ fn argmax_f32() {
+ let pli = Pipeline::<Dna, _>::dispatch();
+ super::test_argmax_f32(&pli);
+ }
+
+ #[test]
+ fn scanner_max() {
+ let generic = Pipeline::generic();
+
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+ let mut striped = generic.stripe(encoded);
+
+ let bg = Background::<Dna>::uniform();
+ let cm = PATTERNS
+ .iter()
+ .map(EncodedSequence::encode)
+ .map(Result::unwrap)
+ .collect::<Result<CountMatrix<Dna>, _>>()
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+
+ striped.configure(&pssm);
+ let scores: StripedScores<f32, _> = generic.score(&pssm, &striped);
+ let best = scores
+ .unstripe()
+ .iter()
+ .cloned()
+ .enumerate()
+ .max_by(|x, y| x.1.partial_cmp(&y.1).unwrap())
+ .unwrap();
+
+ let m = Scanner::new(&pssm, &striped).max().unwrap();
+ assert_eq!(m.position, best.0);
+ assert_eq!(m.score, best.1);
+ }
+}
+
+#[cfg(target_feature = "sse2")]
+mod sse2 {
+ use super::*;
+
+ #[test]
+ fn argmax_f32() {
+ let pli = Pipeline::<Dna, _>::sse2().unwrap();
+ super::test_argmax_f32::<U16, _>(&pli);
+ super::test_argmax_f32::<U32, _>(&pli);
+ }
+}
+
+#[cfg(target_feature = "avx2")]
+mod avx2 {
+ use super::*;
+
+ #[test]
+ fn argmax_f32() {
+ let pli = Pipeline::<Dna, _>::avx2().unwrap();
+ super::test_argmax_f32(&pli);
+ }
+}
+
+#[cfg(target_feature = "neon")]
+mod neon {
+ use super::*;
+
+ #[test]
+ fn argmax_f32() {
+ let pli = Pipeline::<Dna, _>::neon().unwrap();
+ super::test_argmax_f32::<U16, _>(&pli);
+ super::test_argmax_f32::<U32, _>(&pli);
+ }
+}
--
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