From 0a587d21b444abcd6861bf99959e9d2f0f64f22e Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Mon, 24 Jun 2024 14:48:49 +0200
Subject: [PATCH] Add naive baseline implementation to `dna.rs` benchmark in
`lightmotif-bench`
---
lightmotif-bench/dna.rs | 37 ++++++++++++++++++++++++++++++++++++-
1 file changed, 36 insertions(+), 1 deletion(-)
diff --git a/lightmotif-bench/dna.rs b/lightmotif-bench/dna.rs
index 79c77ed..66383e4 100644
--- a/lightmotif-bench/dna.rs
+++ b/lightmotif-bench/dna.rs
@@ -232,10 +232,45 @@ mod external {
)
.unwrap();
- bencher.bytes = seq.len() as u64;
let mut best = 0;
+ bencher.bytes = seq.len() as u64;
bencher.iter(|| best = test::black_box(pssm.score(seq.as_bytes()).unwrap()).loc);
println!("best: {:?}", best);
+ assert_eq!(best, 391677);
+ }
+
+ #[bench]
+ fn naive(bencher: &mut test::Bencher) {
+ let seq = &SEQUENCE[..N];
+ let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
+
+ let bg = Background::<Dna>::uniform();
+ let cm = CountMatrix::<Dna>::from_sequences([
+ EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
+ EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
+ ])
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pssm = pbm.to_scoring(bg);
+
+ let mut best = 0;
+ bencher.bytes = seq.len() as u64;
+ bencher.iter(|| {
+ best = 0;
+ let mut score_best = -f32::INFINITY;
+ for i in 0..encoded.len() - pssm.len() + 1 {
+ let mut score = 0.0;
+ for j in 0..pssm.len() {
+ score += pssm.matrix()[j][encoded[i + j] as usize];
+ }
+ if score > score_best {
+ score_best = score;
+ best = i;
+ }
+ }
+ });
+
+ assert_eq!(best, 391677);
}
}
--
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