Fasta: add new implementation of rust version

bench/algorithm/fasta/6.rs

@@ -0,0 +1,167 @@
+// Ported from 1.zig
+
+use std::io::{self, BufWriter, StdoutLock, Write};
+
+const MAX_LINE_LENGTH: usize = 60;
+const IM: u32 = 139968;
+const IA: u32 = 3877;
+const IC: u32 = 29573;
+
+struct AminoAcid {
+    l: u8,
+    p: f64,
+}
+
+struct Random {
+    seed: u32,
+}
+
+impl Random {
+    fn new() -> Self {
+        Self { seed: 42 }
+    }
+
+    fn next(&mut self) -> f64 {
+        self.seed = (self.seed * IA + IC) % IM;
+        (IM as f64 * self.seed as f64) / IM as f64
+    }
+}
+
+impl Iterator for Random {
+    type Item = f64;
+
+    fn next(&mut self) -> Option<Self::Item> {
+        Some(self.next())
+    }
+}
+
+fn repeat_and_wrap(
+    out: &mut BufWriter<StdoutLock<'static>>,
+    sequence: &[u8],
+    count: usize,
+) -> io::Result<()> {
+    let n = sequence.len();
+    let padded_sequence = (0..(n + MAX_LINE_LENGTH))
+        .map(|i| sequence[i % n])
+        .collect::<Vec<_>>();
+
+    let mut off = 0;
+    let mut idx = 0;
+    while idx < count {
+        let rem = count - idx;
+        let line_length = MAX_LINE_LENGTH.min(rem);
+        out.write_all(&padded_sequence[off..off + line_length])?;
+        out.write_all(&[b'\n'])?;
+
+        off += line_length;
+        if off > n {
+            off -= n;
+        }
+        idx += line_length;
+    }
+    Ok(())
+}
+
+fn generate_and_wrap(
+    random: &mut Random,
+    out: &mut BufWriter<StdoutLock<'static>>,
+    nucleotides: &[AminoAcid],
+    count: usize,
+) -> io::Result<()> {
+    let mut cum_prob = 0.0;
+    let cum_prob_total = nucleotides
+        .iter()
+        .map(|&AminoAcid { l: _, p }| {
+            cum_prob += p;
+            cum_prob * IM as f64
+        })
+        .collect::<Vec<_>>();
+
+    let mut line = [0u8; MAX_LINE_LENGTH + 1];
+    line[MAX_LINE_LENGTH] = b'\n';
+
+    let mut idx = 0;
+    while idx < count {
+        let rem = count - idx;
+        let line_length = MAX_LINE_LENGTH.min(rem);
+
+        line[..line_length]
+            .iter_mut()
+            .zip(&mut *random)
+            .for_each(|(col, r)| {
+                let c = cum_prob_total
+                    .iter()
+                    .fold(0, |acc, &n| acc + (n <= r) as usize);
+
+                *col = nucleotides[c].l;
+            });
+
+        line[line_length] = b'\n';
+        out.write_all(&line[..line_length + 1])?;
+        idx += line_length;
+    }
+    Ok(())
+}
+
+pub fn main() -> io::Result<()> {
+    let stdout = io::stdout();
+    let mut stdout = io::BufWriter::new(stdout.lock());
+    let n = std::env::args_os()
+        .nth(1)
+        .and_then(|s| s.as_os_str().to_str().and_then(|s| s.parse().ok()))
+        .unwrap_or(1000);
+
+    let homo_sapiens_alu =
+        b"GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTC\
+AGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCG\
+TGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGG\
+AGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAA";
+
+    stdout.write_all(b">ONE Homo sapiens alu\n".as_slice())?;
+    repeat_and_wrap(&mut stdout, &homo_sapiens_alu[..], 2 * n)?;
+    let mut random = Random::new();
+
+    let iub_nucleotide_info = &[
+        AminoAcid { l: b'a', p: 0.27 },
+        AminoAcid { l: b'c', p: 0.12 },
+        AminoAcid { l: b'g', p: 0.12 },
+        AminoAcid { l: b't', p: 0.27 },
+        AminoAcid { l: b'B', p: 0.02 },
+        AminoAcid { l: b'D', p: 0.02 },
+        AminoAcid { l: b'H', p: 0.02 },
+        AminoAcid { l: b'K', p: 0.02 },
+        AminoAcid { l: b'M', p: 0.02 },
+        AminoAcid { l: b'N', p: 0.02 },
+        AminoAcid { l: b'R', p: 0.02 },
+        AminoAcid { l: b'S', p: 0.02 },
+        AminoAcid { l: b'V', p: 0.02 },
+        AminoAcid { l: b'W', p: 0.02 },
+        AminoAcid { l: b'Y', p: 0.02 },
+    ];
+
+    stdout.write_all(b">TWO IUB ambiguity codes\n".as_slice())?;
+    generate_and_wrap(&mut random, &mut stdout, iub_nucleotide_info, 3 * n)?;
+
+    let homo_sapien_nucleotide_info = &[
+        AminoAcid {
+            l: b'a',
+            p: 0.3029549426680,
+        },
+        AminoAcid {
+            l: b'c',
+            p: 0.1979883004921,
+        },
+        AminoAcid {
+            l: b'g',
+            p: 0.1975473066391,
+        },
+        AminoAcid {
+            l: b't',
+            p: 0.3015094502008,
+        },
+    ];
+
+    stdout.write_all(b">THREE Homo sapiens frequency\n".as_slice())?;
+    generate_and_wrap(&mut random, &mut stdout, homo_sapien_nucleotide_info, 5 * n)?;
+    Ok(())
+}

bench/bench_rust.yaml

@@ -32,6 +32,7 @@ problems:
       - 1c.rs
       - 5-m.rs
       - 5c-m.rs
+      - 6.rs
   - name: knucleotide
     source:
       - 8.rs