From cd75a9053ba41fbeb953df03944effd309fabf7f Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Fri, 21 Jun 2024 00:55:51 +0200
Subject: [PATCH] Add unit tests for `lightmotif::scan::Scanner`
---
lightmotif/src/scan.rs | 67 +++++++++++++++++++++++++++++++++++++++++-
1 file changed, 66 insertions(+), 1 deletion(-)
diff --git a/lightmotif/src/scan.rs b/lightmotif/src/scan.rs
index 6a5428b..07ce441 100644
--- a/lightmotif/src/scan.rs
+++ b/lightmotif/src/scan.rs
@@ -181,7 +181,7 @@ where
.into_iter()
.max_by(|x, y| x.score.partial_cmp(&y.score).unwrap())
.unwrap_or(Hit::new(0, f32::MIN));
- let mut best_discrete = self.dm.scale(best.score);
+ let mut best_discrete = self.dm.scale(best.score.max(self.threshold));
while self.row < self.seq.matrix().rows() {
let end = (self.row + self.block_size).min(self.seq.matrix().rows() - self.seq.wrap());
self.pipeline
@@ -203,3 +203,68 @@ where
Some(best)
}
}
+
+#[cfg(test)]
+mod test {
+ use super::*;
+ use crate::abc::Dna;
+ use crate::pli::Stripe;
+ use crate::pwm::CountMatrix;
+ use crate::pwm::ScoringMatrix;
+ use crate::seq::EncodedSequence;
+
+ const SEQUENCE: &str = "ATGTCCCAACAACGATACCCCGAGCCCATCGCCGTCATCGGCTCGGCATGCAGATTCCCAGGCG";
+ const PATTERNS: &[&str] = &["GTTGACCTTATCAAC", "GTTGATCCAGTCAAC"];
+
+ fn seq<C: StrictlyPositive>() -> StripedSequence<Dna, C> {
+ let encoded = EncodedSequence::<Dna>::encode(SEQUENCE).unwrap();
+ Pipeline::generic().stripe(encoded)
+ }
+
+ fn pssm() -> ScoringMatrix<Dna> {
+ let cm = CountMatrix::<Dna>::from_sequences(
+ PATTERNS.iter().map(|x| EncodedSequence::encode(x).unwrap()),
+ )
+ .unwrap();
+ let pbm = cm.to_freq(0.1);
+ let pwm = pbm.to_weight(None);
+ pwm.to_scoring()
+ }
+
+ #[test]
+ fn test_collect() {
+ let pssm = self::pssm();
+ let mut striped = self::seq();
+ striped.configure(&pssm);
+
+ let mut scanner = Scanner::new(&pssm, &striped);
+ scanner.threshold(-10.0);
+
+ let mut hits = scanner.collect::<Vec<_>>();
+ assert_eq!(hits.len(), 3);
+
+ hits.sort_by_key(|hit| hit.position);
+ assert_eq!(hits[0].position, 18);
+ assert_eq!(hits[1].position, 27);
+ assert_eq!(hits[2].position, 32);
+ }
+
+ #[test]
+ fn test_max() {
+ let pssm = self::pssm();
+ let mut striped = self::seq();
+ striped.configure(&pssm);
+
+ let mut scanner = Scanner::new(&pssm, &striped);
+ scanner.threshold(-10.0);
+
+ let hit = scanner.max().unwrap();
+ assert!(
+ (hit.score - -5.50167).abs() < 1e-5,
+ "{} != {}",
+ hit.score,
+ -5.50167
+ );
+ assert_eq!(hit.position, 18);
+ }
+}
--
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