Skip to content
Snippets Groups Projects
Commit 45099ad0 authored by Martin Larralde's avatar Martin Larralde
Browse files

Refactor `dna.rs` code in `lightmotif-bench`

parent 41a6d1f7
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
lightmotif-bench/dna.rs
+ 205
− 171
View file @ 45099ad0
#![feature(test)] #![feature(test)]
#[cfg(feature = "bio")]
extern crate bio; extern crate bio;
extern crate lightmotif; extern crate lightmotif;
extern crate test; extern crate test;
...@@ -22,186 +21,221 @@ use lightmotif::seq::EncodedSequence; ...@@ -22,186 +21,221 @@ use lightmotif::seq::EncodedSequence;
const SEQUENCE: &str = include_str!("../lightmotif/benches/ecoli.txt"); const SEQUENCE: &str = include_str!("../lightmotif/benches/ecoli.txt");
const N: usize = SEQUENCE.len() / 10; const N: usize = SEQUENCE.len() / 10;
#[bench] mod scanner {
fn bench_scanner_max_by(bencher: &mut test::Bencher) { use super::*;
let seq = &SEQUENCE[..N];
let encoded = EncodedSequence::<Dna>::encode(seq).unwrap(); /// Bench how long `Scanner::max_by` takes to find the highest hit using
let mut striped = Pipeline::generic().stripe(encoded); /// the score as a comparison key.
#[bench]
let bg = Background::<Dna>::uniform(); fn max_by(bencher: &mut test::Bencher) {
let cm = CountMatrix::<Dna>::from_sequences([ let seq = &SEQUENCE[..N];
EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(), let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(), let mut striped = Pipeline::generic().stripe(encoded);
])
.unwrap(); let bg = Background::<Dna>::uniform();
let pbm = cm.to_freq(0.1); let cm = CountMatrix::<Dna>::from_sequences([
let pssm = pbm.to_scoring(bg); EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
striped.configure(&pssm); ])
let mut best = 0; .unwrap();
bencher.iter(|| { let pbm = cm.to_freq(0.1);
best = Scanner::new(&pssm, &striped) let pssm = pbm.to_scoring(bg);
.max_by(|x, y| x.score.partial_cmp(&y.score).unwrap())
.unwrap() striped.configure(&pssm);
.position; bencher.iter(|| {
}); Scanner::new(&pssm, &striped).max_by(|x, y| x.score.partial_cmp(&y.score).unwrap());
bencher.bytes = seq.len() as u64; });
bencher.bytes = seq.len() as u64;
println!("best: {:?}", best); }
/// Bench how long `Scanner::max` takes to find the highest hit using
/// the custom implementation of `Iterator::max` sorting hits by score
/// and position keys.
#[bench]
fn max(bencher: &mut test::Bencher) {
let seq = &SEQUENCE[..N];
let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
let mut striped = Pipeline::generic().stripe(encoded);
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);
striped.configure(&pssm);
bencher.iter(|| Scanner::new(&pssm, &striped).max().unwrap());
bencher.bytes = seq.len() as u64;
}
} }
#[bench] mod f32 {
fn bench_scanner_best(bencher: &mut test::Bencher) { use super::*;
let seq = &SEQUENCE[..N];
let encoded = EncodedSequence::<Dna>::encode(seq).unwrap(); /// Bench how long `Pipeline::score` and `Pipeline::argmax` take for
let mut striped = Pipeline::generic().stripe(encoded); /// an arbitrary pipeline.
fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>>(
let bg = Background::<Dna>::uniform(); bencher: &mut test::Bencher,
let cm = CountMatrix::<Dna>::from_sequences([ pli: &P,
EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(), ) {
EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(), let seq = &SEQUENCE[..N];
]) let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
.unwrap(); let mut striped = Pipeline::generic().stripe(encoded);
let pbm = cm.to_freq(0.1);
let pssm = pbm.to_scoring(bg); let bg = Background::<Dna>::uniform();
let cm = CountMatrix::<Dna>::from_sequences([
striped.configure(&pssm); EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
let mut best = 0; EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
bencher.iter(|| best = Scanner::new(&pssm, &striped).max().unwrap().position); ])
bencher.bytes = seq.len() as u64; .unwrap();
let pbm = cm.to_freq(0.1);
println!("best: {:?}", best); let pssm = pbm.to_scoring(bg);
striped.configure(&pssm);
let mut scores = StripedScores::empty();
scores.resize(striped.matrix().rows(), striped.len());
bencher.bytes = seq.len() as u64;
bencher.iter(|| {
test::black_box(pli.score_into(&pssm, &striped, &mut scores));
scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
});
}
/// Bench how long `Pipeline::<_, Generic>` takes.
#[bench]
fn generic(bencher: &mut test::Bencher) {
let pli = Pipeline::generic();
bench_lightmotif::<U1, _>(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Sse2>` takes.
#[cfg(target_feature = "sse2")]
#[bench]
fn sse2(bencher: &mut test::Bencher) {
let pli = Pipeline::sse2().unwrap();
bench_lightmotif::<U16, _>(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Dispatch>` takes.
#[bench]
fn dispatch(bencher: &mut test::Bencher) {
let pli = Pipeline::dispatch();
bench_lightmotif(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Avx2>` takes.
#[cfg(target_feature = "avx2")]
#[bench]
fn avx2(bencher: &mut test::Bencher) {
let pli = Pipeline::avx2().unwrap();
bench_lightmotif(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Neon>` takes.
#[cfg(target_feature = "neon")]
#[bench]
fn neon(bencher: &mut test::Bencher) {
let pli = Pipeline::neon().unwrap();
bench_lightmotif(bencher, &pli);
}
} }
fn bench_lightmotif<C: StrictlyPositive, P: Score<f32, Dna, C> + Maximum<f32, C>>( mod u8 {
bencher: &mut test::Bencher, use super::*;
pli: &P,
) { /// Bench how long `Pipeline::score` and `Pipeline::argmax` take for
let seq = &SEQUENCE[..N]; /// an arbitrary pipeline using discrete scores.
let encoded = EncodedSequence::<Dna>::encode(seq).unwrap(); fn bench_lightmotif_discrete<C: StrictlyPositive, P: Score<u8, Dna, C> + Maximum<u8, C>>(
let mut striped = Pipeline::generic().stripe(encoded); bencher: &mut test::Bencher,
pli: &P,
let bg = Background::<Dna>::uniform(); ) {
let cm = CountMatrix::<Dna>::from_sequences([ let seq = &SEQUENCE[..N];
EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(), let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(), let mut striped = Pipeline::generic().stripe(encoded);
])
.unwrap(); let bg = Background::<Dna>::uniform();
let pbm = cm.to_freq(0.1); let cm = CountMatrix::<Dna>::from_sequences([
let pssm = pbm.to_scoring(bg); EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
striped.configure(&pssm); ])
let mut scores = StripedScores::empty(); .unwrap();
scores.resize(striped.matrix().rows(), striped.len()); let pbm = cm.to_freq(0.1);
bencher.bytes = seq.len() as u64; let pssm = pbm.to_scoring(bg);
let mut best = 0; let dm = pssm.to_discrete();
bencher.iter(|| {
test::black_box(pli.score_into(&pssm, &striped, &mut scores)); striped.configure(&pssm);
best = scores.offset(test::black_box(pli.argmax(&scores).unwrap())); let mut scores = StripedScores::empty();
}); scores.resize(striped.matrix().rows(), striped.len());
bencher.bytes = seq.len() as u64;
println!("best: {:?}", best); bencher.iter(|| {
test::black_box(pli.score_into(&dm, &striped, &mut scores));
scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
});
}
/// Bench how long `Pipeline::<_, Generic>` takes using `u8` scores.
#[bench]
fn generic(bencher: &mut test::Bencher) {
let pli = Pipeline::generic();
bench_lightmotif_discrete::<U1, _>(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Sse2>` takes using `u8` scores.
#[cfg(target_feature = "sse2")]
#[bench]
fn sse2(bencher: &mut test::Bencher) {
let pli = Pipeline::sse2().unwrap();
bench_lightmotif_discrete::<U16, _>(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Generic>` takes using `u8` scores.
#[bench]
fn dispatch(bencher: &mut test::Bencher) {
let pli = Pipeline::dispatch();
bench_lightmotif_discrete(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Generic>` takes using `u8` scores.
#[cfg(target_feature = "avx2")]
#[bench]
fn avx2(bencher: &mut test::Bencher) {
let pli = Pipeline::avx2().unwrap();
bench_lightmotif_discrete(bencher, &pli);
}
/// Bench how long `Pipeline::<_, Neon>` takes using `u8` scores.
#[cfg(target_feature = "neon")]
#[bench]
fn neon(bencher: &mut test::Bencher) {
let pli = Pipeline::neon().unwrap();
bench_lightmotif_discrete(bencher, &pli);
}
} }
fn bench_lightmotif_discrete<C: StrictlyPositive, P: Score<u8, Dna, C> + Maximum<u8, C>>( mod external {
bencher: &mut test::Bencher,
pli: &P,
) {
let seq = &SEQUENCE[..N];
let encoded = EncodedSequence::<Dna>::encode(seq).unwrap();
let mut striped = Pipeline::generic().stripe(encoded);
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 dm = pssm.to_discrete();
striped.configure(&pssm);
let mut scores = StripedScores::empty();
let mut best = 0;
scores.resize(striped.matrix().rows(), striped.len());
bencher.bytes = seq.len() as u64;
bencher.iter(|| {
test::black_box(pli.score_into(&dm, &striped, &mut scores));
best = scores.offset(test::black_box(pli.argmax(&scores).unwrap()));
});
println!("best: {:?}", best);
}
#[bench]
fn bench_generic(bencher: &mut test::Bencher) {
let pli = Pipeline::generic();
bench_lightmotif::<U1, _>(bencher, &pli);
}
#[cfg(target_feature = "sse2")]
#[bench]
fn bench_sse2(bencher: &mut test::Bencher) {
let pli = Pipeline::sse2().unwrap();
bench_lightmotif::<U16, _>(bencher, &pli);
}
#[bench]
fn bench_dispatch(bencher: &mut test::Bencher) {
let pli = Pipeline::dispatch();
bench_lightmotif(bencher, &pli);
}
#[cfg(target_feature = "avx2")]
#[bench]
fn bench_avx2(bencher: &mut test::Bencher) {
let pli = Pipeline::avx2().unwrap();
bench_lightmotif(bencher, &pli);
}
#[bench]
fn bench_discrete_generic(bencher: &mut test::Bencher) {
let pli = Pipeline::generic();
bench_lightmotif_discrete::<U1, _>(bencher, &pli);
}
#[cfg(target_feature = "sse2")]
#[bench]
fn bench_discrete_sse2(bencher: &mut test::Bencher) {
let pli = Pipeline::sse2().unwrap();
bench_lightmotif_discrete::<U16, _>(bencher, &pli);
}
#[bench]
fn bench_discrete_dispatch(bencher: &mut test::Bencher) {
let pli = Pipeline::dispatch();
bench_lightmotif_discrete(bencher, &pli);
}
#[cfg(target_feature = "avx2")] use super::*;
#[bench]
fn bench_discrete_avx2(bencher: &mut test::Bencher) {
let pli = Pipeline::avx2().unwrap();
bench_lightmotif_discrete(bencher, &pli);
}
#[bench] #[bench]
fn bench_bio(bencher: &mut test::Bencher) { fn bio(bencher: &mut test::Bencher) {
use bio::pattern_matching::pssm::DNAMotif; use bio::pattern_matching::pssm::DNAMotif;
use bio::pattern_matching::pssm::Motif; use bio::pattern_matching::pssm::Motif;
let seq = &SEQUENCE[..N]; let seq = &SEQUENCE[..N];
let pssm = DNAMotif::from_seqs( let pssm = DNAMotif::from_seqs(
vec![b"GTTGACCTTATCAAC".to_vec(), b"GTTGATCCAGTCAAC".to_vec()].as_ref(), vec![b"GTTGACCTTATCAAC".to_vec(), b"GTTGATCCAGTCAAC".to_vec()].as_ref(),
None, None,
) )
.unwrap(); .unwrap();
bencher.bytes = seq.len() as u64; bencher.bytes = seq.len() as u64;
let mut best = 0; let mut best = 0;
bencher.iter(|| best = test::black_box(pssm.score(seq.as_bytes()).unwrap()).loc); bencher.iter(|| best = test::black_box(pssm.score(seq.as_bytes()).unwrap()).loc);
println!("best: {:?}", best); println!("best: {:?}", best);
}
} }
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment