Add FASTA benchmarks

Cargo.toml

@@ -17,5 +17,5 @@ path = "src/lib.rs"
 criterion = "0.5.1"
 
 [[bench]]
-name = "sequence_benchmark"
+name = "all_benchmark"
 harness = false

benches/all_benchmark.rs

@@ -0,0 +1,8 @@
+use criterion::criterion_main;
+
+mod benchmarks;
+
+criterion_main! {
+    benchmarks::fasta_benchmark::fasta_benches,
+    benchmarks::dna_benchmark::dna_benches,
+}

benches/sequence_benchmark.rs → benches/benchmarks/dna_benchmark.rs

@@ -1,4 +1,4 @@
-use criterion::{criterion_group, criterion_main, Criterion};
+use criterion::{criterion_group, Criterion};
 use nuc::dna::Dna;
 
 pub fn counting_nucleotides_benchmark(c: &mut Criterion) {
@@ -11,5 +11,4 @@ pub fn reverse_complement_benchmark(c: &mut Criterion) {
     c.bench_function("create the reverse complement", |b| b.iter(|| dna.rc()));
 }
 
-criterion_group!(benches, counting_nucleotides_benchmark, reverse_complement_benchmark);
-criterion_main!(benches);
+criterion_group!(dna_benches, counting_nucleotides_benchmark, reverse_complement_benchmark);

benches/benchmarks/fasta_benchmark.rs

@@ -0,0 +1,15 @@
+use std::fs::File;
+
+use criterion::{criterion_group, Criterion};
+use nuc::fasta::FastaReader;
+
+pub fn parsing_chromosome1_benchmark(c: &mut Criterion) {
+    c.bench_function("parsing a random 3MB FASTA file", |b| {
+        b.iter(|| {
+            let reader = FastaReader::new(File::open("benches/random.fa").unwrap());
+            assert_eq!(reader.into_iter().count(), 13);
+        })
+    });
+}
+
+criterion_group!(fasta_benches, parsing_chromosome1_benchmark);

benches/benchmarks/mod.rs

@@ -0,0 +1,2 @@
+pub mod fasta_benchmark;
+pub mod dna_benchmark;

src/dna.rs

@@ -118,7 +118,6 @@ impl Dna {
             dna.nucleotides[i] = hash_chars_be(b);
             i += 1;
         }
-        dbg!(&dna);
 
         dna
     }

src/fasta.rs

@@ -17,7 +17,6 @@ impl<R: Read + std::fmt::Debug> Iterator for FastaReader<R> {
     type Item = FastaDna;
 
     fn next(&mut self) -> Option<Self::Item> {
-        println!("next:");
         let mut id = self.next_id.take().unwrap_or_default();
         let mut sequence = String::with_capacity(1000);
 

tests/fasta_test.rs

@@ -44,10 +44,3 @@ fn can_read_an_empty_fasta_file() {
     let records = FastaReader::new("".as_bytes()).into_iter().collect::<Vec<_>>();
     assert_eq!(records, vec![]);
 }
-
-#[test]
-fn read_chromosome1() {
-    let reader = FastaReader::new(File::open("/home/fbull/test.fa").unwrap());
-
-    assert_eq!(reader.into_iter().count(), 1);
-}