feat: add generation function for fast[a|q] format

.copier-answers.yml

@@ -13,5 +13,5 @@ forge_namespace: natir
 forge_repo_name: biotest
 msrv: '1.75'
 proc_macro: true
-project_description: Many function to generate test data for bioinformatics data
+project_description: Generate random test data for bioinformatics
 project_name: biotest

Cargo.toml

@@ -3,7 +3,7 @@ name = "biotest"
 version = "0.1.0"
 authors = ["Pierre Marijon <[email protected]>"]
 edition = "2021"
-description = "Many function to generate test data for bioinformatics data"
+description = "Generate random test data for bioinformatics"
 rust-version = "1.75"
 
 homepage = "https://github.com/natir/biotest"
@@ -15,12 +15,11 @@ license-file = "LICENSE"
 
 
 [dependencies]
-
+rand           = { version = "0.8" }
 
 # Error management
 thiserror      = { version = "1" }
 
-
 # Logging and error management
 log            = { version = "0.4" }
 
@@ -30,12 +29,15 @@ biotest_derive = { path = "biotest_derive", optional = true }
 
 [dev-dependencies]
 criterion      = { version = "0.5" }
+tempfile       = { version = "3" }
 
 # CLI management
 clap           = { version = "4", features = ["derive"] }
 
 # Logging management
 stderrlog      = { version = "0.5" }
+
+
 [profile.release]
 lto = 'thin'
 opt-level = 3
@@ -46,4 +48,4 @@ incremental = false
 
 [profile.profiling]
 inherits = "release"
-debug = true
+debug = true

Readme.md

@@ -2,21 +2,15 @@
 
 [![License](https://img.shields.io/badge/license-MIT-green)](https:///natir/biotest/blob/master/LICENSE)
 
+Generate random test data for bioinformatics
 
-Many function to generate test data for bioinformatics data
-
-## Installation
-
-### From source
+## Usage
 
-```bash
-git clone https:///natir/biotest.git
-cd biotest
-cargo install --path .
+In your Cargo.toml add
+```toml
+biotest = { url = "https:///natir/biotest.git" }
 ```
 
-## Usage
-
 ## Minimum supported Rust version
 
 Currently the minimum supported Rust version is 1.75.

biotest_derive/src/lib.rs

@@ -1,4 +1,4 @@
-//! Many function to generate test data for bioinformatics data procedural macro crate
+//! Generate random test data for bioinformatics"
 
 #![warn(missing_docs)]
 

src/constants.rs

@@ -0,0 +1,70 @@
+//! Declarations of some constants value
+
+/* std use */
+
+/* crates use */
+
+/* projet use */
+
+const fn gen_array<const N: usize, const B: usize>() -> [u8; N] {
+    let mut array = [0; N];
+
+    let mut i = 0;
+    while i < N {
+        array[i] = (B + i) as u8;
+        i += 1;
+    }
+
+    array
+}
+
+/// Fixed random seed
+pub const SEED: [u8; 32] = [42; 32];
+
+/// Nucleotides with any case
+pub const NUCLEOTIDES: [u8; 8] = *b"ACTGactg";
+
+/// Nucleotides lower
+pub const NUCLEOTIDES_LOWER: [u8; 4] = *b"actg";
+
+/// Nucleotides upper
+pub const NUCLEOTIDES_UPPER: [u8; 4] = *b"ACTG";
+
+/// All possible phred 33 value
+pub const PHRED33: [u8; 40] = gen_array::<40, 33>();
+
+/// All possible phred 64 value
+pub const PHRED64: [u8; 40] = gen_array::<40, 64>();
+
+/// Alphabets with [ \ ] ^ _ `
+pub const ALPHABETS: [u8; 58] = gen_array::<58, 65>();
+
+#[cfg(test)]
+mod tests {
+    /* project use */
+    use super::*;
+
+    #[test]
+    fn phred33() {
+        assert_eq!(
+            gen_array::<40, 33>().to_vec(),
+            b"!\"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGH".to_vec()
+        );
+    }
+
+    #[test]
+    fn phred64() {
+        assert_eq!(
+            gen_array::<40, 64>().to_vec(),
+            b"@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefg".to_vec()
+        );
+    }
+
+    #[test]
+    fn alphapets() {
+        assert_eq!(
+            gen_array::<58, 65>().to_vec(),
+            b"ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuvwxyz".to_vec()
+        );
+    }
+}

src/error.rs

@@ -6,7 +6,9 @@ use thiserror;
 /// Enum to manage error
 #[derive(std::fmt::Debug, thiserror::Error)]
 pub enum Error {
-    }
+    #[error(transparent)]
+    StdIo(#[from] std::io::Error),
+}
 
 /// Alias of result
 pub type Result<T> = core::result::Result<T, Error>;

src/format.rs

@@ -0,0 +1,11 @@
+//! Format data generation
+
+/* std use */
+
+/* crates use */
+
+/* module declaration */
+pub mod fasta;
+pub mod fastq;
+
+/* projet use */

src/format/fasta.rs

@@ -0,0 +1,149 @@
+//! Fasta generation
+
+/* std use */
+use std::io::Write;
+
+/* crates use */
+
+/* projet use */
+use crate::constants;
+use crate::error;
+
+fn description<W>(
+    output: &mut W,
+    rng: &mut rand::rngs::StdRng,
+    id: usize,
+    comment: usize,
+) -> error::Result<()>
+where
+    W: std::io::Write,
+{
+    output.write_all(&[b'>'])?;
+    crate::text(output, rng, id)?;
+    output.write_all(&[b' '])?;
+    crate::text(output, rng, comment)?;
+
+    Ok(())
+}
+
+/// Write record
+pub fn record<W>(
+    output: &mut W,
+    rng: &mut rand::rngs::StdRng,
+    id: usize,
+    comment: usize,
+    seq_len: usize,
+) -> error::Result<()>
+where
+    W: std::io::Write,
+{
+    description(output, rng, id, comment)?;
+    output.write_all(&[b'\n'])?;
+    crate::sequence(output, rng, seq_len)?;
+
+    Ok(())
+}
+
+/// Write multiple record
+pub fn records<W>(
+    output: &mut W,
+    rng: &mut rand::rngs::StdRng,
+    id: usize,
+    comment: usize,
+    seq_len: usize,
+    num_record: usize,
+) -> error::Result<()>
+where
+    W: std::io::Write,
+{
+    for _ in 0..num_record {
+        record(output, rng, id, comment, seq_len)?;
+        output.write_all(&[b'\n'])?;
+    }
+
+    Ok(())
+}
+
+/// Create a fasta file
+pub fn create<P>(
+    path: P,
+    rng: &mut rand::rngs::StdRng,
+    id: usize,
+    comment: usize,
+    seq_len: usize,
+    num_record: usize,
+) -> error::Result<()>
+where
+    P: std::convert::AsRef<std::path::Path>,
+{
+    let mut output = std::fs::File::create(&path)?;
+
+    records(&mut output, rng, id, comment, seq_len, num_record)?;
+
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    /* std use */
+    use std::io::Read;
+
+    /* project use */
+    use super::*;
+
+    const TRUTH: &[u8] = b">oNi_P dzwC[tBTlD
+tCGCgtGTTAGTTAagccAcggtAatGcTtgtaCgcAGgAtaTcgAAtTa
+>rQ_[V S^RtSvzMeT
+ttGCtCatGtctgCTGGTACtgTgcaaaagggGAGacAtgCtGCAAtTac
+>HYNm[ QBCgL`Scxx
+GGtatTCaTCctcTGgAActTgCGAcaAgaAAtaTCCcAgagggaCcttC
+>gNXcb hRd]QWyFOg
+gAACcTtCttAacGtTtAtGTgACAGCCaCGctGagattTGtgCttaAGg
+>ppugI LwOFhYRxBZ
+CTGTCCACgTTTGagtGaGCatAGGACAAaacTaTTagagGtatAGCcTa
+";
+
+    #[test]
+    fn record_() -> error::Result<()> {
+        let mut output = Vec::new();
+        let mut rng = crate::rand();
+
+        record(&mut output, &mut rng, 5, 10, 50)?;
+
+        assert_eq!(output, TRUTH.to_vec()[..68]);
+
+        Ok(())
+    }
+
+    #[test]
+    fn records_() -> error::Result<()> {
+        let mut output = Vec::new();
+        let mut rng = crate::rand();
+
+        records(&mut output, &mut rng, 5, 10, 50, 5)?;
+
+        assert_eq!(output, TRUTH);
+
+        Ok(())
+    }
+
+    #[test]
+    fn create_() -> error::Result<()> {
+        let mut rng = crate::rand();
+
+        let temp_dir = tempfile::tempdir()?;
+        let temp_path = temp_dir.path();
+
+        let temp_file = temp_path.join("tmp.fasta");
+
+        create(&temp_file, &mut rng, 5, 10, 50, 5)?;
+
+        let mut data = Vec::new();
+        let mut input = std::fs::File::open(&temp_file)?;
+        input.read_to_end(&mut data)?;
+
+        assert_eq!(data, TRUTH);
+
+        Ok(())
+    }
+}