biotest 0.2.0

//! Fastq generation
//!
//! Usage:
//! ```no_run
//! use biotest::Format;
//!
//! # fn main() -> Result<(), biotest::error::Error> {
//! let mut rng = biotest::rand(); // Create a random generator with a fixed seed
//!
//! let mut output = Vec::new();
//! let generator = biotest::Fastq::default();
//!
//! generator.record(&mut output, &mut rng)?; // Write one fastq record in output
//! generator.records(&mut output, &mut rng, 5)?; // Write five fastq records in output
//!
//! generator.create("test.fastq", &mut rng, 5)?; // Write five fastq record in "test.fasta"
//! # Ok(())
//! # }
//! ```
//!
//! Read generate follow this template
//! ```no_compile
//! >{id_prefix}{id}{id_suffix} {comment_prefix}{comment}{comment_suffix}
//! {sequence}
//! +{plus_prefix}{plus}{plus_suffix}
//! {quality}
//! ```
//!
//! Many think could be configurable with builder patern:
//! ```no_run
//! use rand;
//! use rand::SeedableRng;
//! use biotest::Format;
//!
//! # fn main() -> Result<(), biotest::error::Error> {
//! let mut rng = rand::rngs::StdRng::from_entropy(); // Create a random generator with a 'random' seed
//!
//! let generator = biotest::Fastq::builder()
//!     .id(biotest::values::Alphabet::Lower) // Set alphabet use to generate sequence id
//!     .id_len(10) // Set length of id
//!     .id_prefix(b"prefix".to_vec()) // Set read id prefix
//!     .id_suffix(b"suffix".to_vec()) // Set read id prefix
//!     .comment(biotest::values::Alphabet::Upper) // Set alphabet use to generate sequence comment
//!     .comment_len(0) // If comment length is set to 0 prefix and suffix isn't write
//!     .comment_prefix(b"prefix".to_vec()) // Set read id prefix
//!     .comment_suffix(b"suffix".to_vec()) // Set read id prefix
//!     .plus(biotest::values::Alphabet::Upper) // Set alphabet use to generate sequence plus
//!     .plus_len(0) // If plus length is set to 0 prefix and suffix isn't write
//!     .plus_prefix(b"prefix".to_vec()) // Set read id prefix
//!     .plus_suffix(b"suffix".to_vec()) // Set read id prefix
//!     .build()?;
//!
//! generator.create("test.fastq", &mut rng, 5)?; // Write five fasta record in "test.fastq"
//! # Ok(())
//! # }
//! ```

/* std use */

/* crates use */

/* projet use */
use crate::error;
use crate::format;
use crate::values;

use crate::values::Generate as _;

/// Struct to generate random fastq record
#[derive(derive_builder::Builder)]
#[builder(pattern = "owned")]
pub struct Fastq {
    /// Alphabet use for id generation
    #[builder(default = "values::Alphabet::Upper")]
    id: values::Alphabet,

    /// Length of id
    #[builder(default = "10")]
    id_len: usize,

    /// Id prefix
    #[builder(default = "b\"\".to_vec()")]
    id_prefix: Vec<u8>,

    /// Id suffix
    #[builder(default = "b\"\".to_vec()")]
    id_suffix: Vec<u8>,

    /// Id weights
    #[builder(default = "vec![1; 0]")]
    id_weights: Vec<u8>,

    /// Alphapet use for comment generation
    #[builder(default = "values::Alphabet::Lower")]
    comment: values::Alphabet,
    /// Comment length
    #[builder(default = "20")]
    comment_len: usize,

    /// Comment prefix
    #[builder(default = "b\"\".to_vec()")]
    comment_prefix: Vec<u8>,

    /// Comment suffix
    #[builder(default = "b\"\".to_vec()")]
    comment_suffix: Vec<u8>,

    /// Comment weights
    #[builder(default = "vec![1; 0]")]
    comment_weights: Vec<u8>,

    /// Alphabet use for sequence generation
    #[builder(default = "values::Nucleotides::Dna")]
    sequence: values::Nucleotides,

    /// Sequence length
    #[builder(default = "150")]
    sequence_len: usize,

    /// Sequence weights
    #[builder(default = "vec![1; 0]")]
    sequence_weights: Vec<u8>,

    /// Alphabet use for plus comment generation
    #[builder(default = "values::Alphabet::A2z")]
    plus: values::Alphabet,

    /// Plus comment len
    #[builder(default = "5")]
    plus_len: usize,

    /// Plus prefix
    #[builder(default = "b\"\".to_vec()")]
    plus_prefix: Vec<u8>,

    /// Plus suffix
    #[builder(default = "b\"\".to_vec()")]
    plus_suffix: Vec<u8>,

    /// Plus weights
    #[builder(default = "vec![1; 0]")]
    plus_weights: Vec<u8>,

    /// Alphabet use for quality generation
    #[builder(default = "values::Quality::Illumina")]
    quality: values::Quality,

    /// Quality weights
    #[builder(default = "vec![1; 0]")]
    quality_weights: Vec<u8>,
}

impl Fastq {
    /// Create a FastqBuilder
    pub fn builder() -> FastqBuilder {
        FastqBuilder::default()
    }
}

impl core::default::Default for Fastq {
    fn default() -> Self {
        FastqBuilder::default().build().unwrap() // it's default no error
    }
}

impl format::Format for Fastq {
    fn header(
        &self,
        _output: &mut dyn std::io::Write,
        _rng: &mut rand::rngs::StdRng,
    ) -> error::Result<()> {
        Ok(())
    }

    fn record(
        &self,
        output: &mut dyn std::io::Write,
        rng: &mut rand::rngs::StdRng,
    ) -> error::Result<()> {
        // id
        output.write_all(&[b'@'])?;
        output.write_all(&self.id_prefix)?;
        if self.id_weights.is_empty() {
            output.write_all(&self.id.generate(rng, self.id_len)?)?;
        } else {
            output.write_all(&self.id.weighted(rng, self.id_len, &self.id_weights)?)?;
        }
        output.write_all(&self.id_suffix)?;
        if self.id_prefix.len() + self.id_len + self.id_suffix.len() != 0 {
            output.write_all(&[b' '])?;
        }

        // comment
        output.write_all(&self.comment_prefix)?;
        if self.comment_weights.is_empty() {
            output.write_all(&self.comment.generate(rng, self.comment_len)?)?;
        } else {
            output.write_all(&self.comment.weighted(
                rng,
                self.comment_len,
                &self.comment_weights,
            )?)?;
        }
        output.write_all(&self.comment_suffix)?;
        output.write_all(b"\n")?;

        // sequence
        if self.sequence_weights.is_empty() {
            output.write_all(&self.sequence.generate(rng, self.sequence_len)?)?;
        } else {
            output.write_all(&self.sequence.weighted(
                rng,
                self.sequence_len,
                &self.sequence_weights,
            )?)?;
        }
        output.write_all(b"\n")?;

        // plus
        output.write_all(b"+")?;
        output.write_all(&self.plus_prefix)?;
        if self.plus_weights.is_empty() {
            output.write_all(&self.plus.generate(rng, self.plus_len)?)?;
        } else {
            output.write_all(&self.plus.weighted(rng, self.plus_len, &self.plus_weights)?)?;
        }
        output.write_all(&self.plus_suffix)?;
        output.write_all(b"\n")?;

        // quality
        if self.quality_weights.is_empty() {
            output.write_all(&self.quality.generate(rng, self.sequence_len)?)?;
        } else {
            output.write_all(&self.quality.weighted(
                rng,
                self.sequence_len,
                &self.quality_weights,
            )?)?;
        }

        Ok(())
    }
}

#[cfg(test)]
mod tests {
    /* std use */
    use std::io::Read as _;

    /* project use */
    use super::format::Format as _;
    use super::*;

    const TRUTH: &[u8] = b"@GSWNP zybhlatbbu
CGCgtGTTAGTTAagccAcggtAatGcTtgtaCgcAGgAtaTcgAAtTaT
+
60D.5-E.F/$*::>A2A>)\'=0B<$E/&411+!)AF,E;7.8.3GF2%\"
@CTQMK tnwbrlpbpv
gCtGCAAtTacCGtTAAcaGGtatTCaTCctcTGgAActTgCGAcaAgaA
+
!B+\':<>3#.EFG@@D\'*98<-:,1+F?>\"?(<C,IA+\'3@\"<%=3>B4-
@TYGTA sulyzaweta
GCCaCGctGagattTGtgCttaAGggTcCTGcGTAGCTGTCCACgTTTGa
+
E/A71C4\'6&!1\"\'!I\")67,8>$$*,:6GIE0@C6B2<7A53478?%I\'
@KWRUD mkpkjusxnd
tgACTacgtCTaTgTCAGgCtaGTtcCCTcgcTgAgGgAtCAAatTCTAT
+
-I2IIGC27.=)(&3=8(A!,=EB-E/HC)-%\'9>0$&&?A/DAIC!1)1
@DPOXN glybtnsmjj
atcaCtGcTAGCCAgaTTgcAaTtaTGgACTTagGgtATACCtcTctCAt
+
E(1)(8E,\'HC4<55;&3!,*$G>A)@H149G@/7.D$$6-CGI5#@$F=
";

    const DEFAULT: &[u8] = b"@GSWNPZYBHL atbbutlfemxuzgaghmwn
gccAcggtAatGcTtgtaCgcAGgAtaTcgAAtTaTaGaTggttGCtCatGtctgCTGGTACtgTgcaaaagggGAGacAtgCtGCAAtTacCGtTAAcaGGtatTCaTCctcTGgAActTgCGAcaAgaAAtaTCCcAgagggaCcttC
+gNXcb
<-:,1+F?>\"?(<C,IA+\'3@\"<%=3>B4-?CG@!GI!(?\"1\'%))7&08<27F?3AA$E(/@A#FBBF<\')G+%2-\"&*C+,\'!&F4,,7E/A71C4\'6&!1\"\'!I\")67,8>$$*,:6GIE0@C6B2<7A53478?%I\'E<@AH5189";

    const WEIGHTED_TRUTH: &[u8] = b"@ECEED cdeeacdeac
GAAGGTCCTGCTGGGTCCGATCCATGTTGAGCCGGTGCAGGTGGACGGTT
+DEDCC
(%))&$)'$)(&##&'*)(*!)*''%%)())'&(!(!'')(&$)')%''&";

    #[test]
    fn default() -> error::Result<()> {
        let mut output = Vec::new();
        let mut rng = crate::rand();

        let generator = Fastq::default();

        generator.record(&mut output, &mut rng)?;

        assert_eq!(output, DEFAULT);

        Ok(())
    }

    #[test]
    fn record() -> error::Result<()> {
        let mut output = Vec::new();
        let mut rng = crate::rand();

        let generator = Fastq::builder()
            .id_len(5)
            .comment_len(10)
            .plus_len(0)
            .sequence_len(50)
            .build()?;

        generator.record(&mut output, &mut rng)?;

        assert_eq!(output, TRUTH.to_vec()[..121]);

        Ok(())
    }

    #[test]
    fn weigthed_record() -> error::Result<()> {
        let mut output = Vec::new();
        let mut rng = crate::rand();

        let generator = Fastq::builder()
            .id_len(5)
            .id_weights(vec![1, 2, 3, 4, 5])
            .comment_len(10)
            .comment_weights(vec![1, 2, 3, 4, 5])
            .sequence_len(50)
            .sequence_weights(vec![1, 2, 3, 4])
            .plus_weights(vec![1, 2, 3, 4, 5])
            .quality_weights(vec![1, 0, 3, 4, 5, 6, 7, 8, 9, 2])
            .build()?;

        generator.record(&mut output, &mut rng)?;

        assert_eq!(output, WEIGHTED_TRUTH.to_vec());

        Ok(())
    }

    #[test]
    fn pre_suf_ix() -> error::Result<()> {
        let mut output = Vec::new();
        let mut rng = crate::rand();

        let generator = Fastq::builder()
            .id_len(5)
            .comment_len(10)
            .plus_len(0)
            .sequence_len(50)
            .id_prefix(b"id_prefix_".to_vec())
            .id_suffix(b"_id_suffix".to_vec())
            .comment_prefix(b"comment_prefix_".to_vec())
            .comment_suffix(b"_comment_suffix".to_vec())
            .plus_prefix(b"plus_prefix_".to_vec())
            .plus_suffix(b"_plus_suffix".to_vec())
            .build()?;

        generator.record(&mut output, &mut rng)?;

        assert_eq!(
            output,
            b"@id_prefix_GSWNP_id_suffix comment_prefix_zybhlatbbu_comment_suffix
CGCgtGTTAGTTAagccAcggtAatGcTtgtaCgcAGgAtaTcgAAtTaT
+plus_prefix__plus_suffix
60D.5-E.F/$*::>A2A>)\'=0B<$E/&411+!)AF,E;7.8.3GF2%\""
                .to_vec()
        );

        Ok(())
    }

    #[test]
    fn records() -> error::Result<()> {
        let mut output = Vec::new();
        let mut rng = crate::rand();

        let generator = Fastq::builder()
            .id_len(5)
            .comment_len(10)
            .plus_len(0)
            .sequence_len(50)
            .build()?;

        generator.records(&mut output, &mut rng, 5)?;

        assert_eq!(output, TRUTH.to_vec());

        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");

        let generator = Fastq::builder()
            .id_len(5)
            .comment_len(10)
            .plus_len(0)
            .sequence_len(50)
            .build()?;

        generator.create(&temp_file, &mut rng, 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.to_vec());

        Ok(())
    }
}