kmerutils 0.0.14

Kmer counting, hashing, sequence sketching
Documentation 
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//! describe sketching paramaters, kmer size, sketching size and sketching algorithms.

use std::io::{BufReader, BufWriter};

use std::fs::OpenOptions;
use std::path::{Path, PathBuf};

use serde::{Deserialize, Serialize};
use serde_json::to_writer;

/// specify if we process DNA sequence or AA sequences
#[derive(Copy, Clone, Serialize, Deserialize, Debug)]
pub enum DataType {
    DNA,
    AA,
}

/// Specify which algo we use for sketching :  Probminhash or SuperMinHash or Hyperloglog (SetSketch) algorithms.  
/// - PROB3A is the value for asking ProbMinHashh3a,
/// - SUPER for first version SuperMinHash.(f64 signature)
/// - SUPER2 for second version of superminhash (u64 signature)
/// - OPTDENS for optimal densification  (u43, u64 , f32 or f64 signature)
/// - REVOPTDENS for optimal densification with small variance in case where there can many sequences smaller than size of sketching. (u43, u64 , f32 or f64 signature)
/// - HLL for SetSketch based on hyperloglog (u16, u32 or more signature)
#[derive(Copy, Clone, Serialize, Deserialize, Debug)]
pub enum SketchAlgo {
    PROB3A,
    SUPER,
    SUPER2,
    OPTDENS,
    REVOPTDENS,
    HLL,
}
// This is redundant with struct Sketcher for DNA case and RNA case, but it makes
// possible the factorization of all parameters

/// describe sketching paramaters, kmer size, sketching size and sketching algorithms.
///
#[derive(Copy, Clone, Serialize, Deserialize, Debug)]
pub struct SeqSketcherParams {
    kmer_size: usize,
    sketch_size: usize,
    algo: SketchAlgo,
    data_t: DataType,
}

impl SeqSketcherParams {
    //
    pub fn new(kmer_size: usize, sketch_size: usize, algo: SketchAlgo, data_t: DataType) -> Self {
        SeqSketcherParams {
            kmer_size,
            sketch_size,
            algo,
            data_t,
        }
    }

    /// returns kmer size
    pub fn get_kmer_size(&self) -> usize {
        self.kmer_size
    }

    /// return sketch size
    pub fn get_sketch_size(&self) -> usize {
        self.sketch_size
    }

    /// get get sketching algorithm PROB or SUPER
    pub fn get_algo(&self) -> SketchAlgo {
        self.algo
    }

    /// returns AA or DNA type for data
    pub fn get_data_t(&self) -> DataType {
        self.data_t
    }

    /// serialized dump
    pub fn dump_json(&self, filename: &String) -> Result<(), String> {
        //
        let filepath = PathBuf::from(filename.clone());
        //
        log::info!("dumping sketching parameters in json file : {}", filename);
        //
        let fileres = OpenOptions::new()
            .write(true)
            .create(true)
            .truncate(true)
            .open(&filepath);
        if fileres.is_err() {
            log::error!(
                "SeqSketcher dump : dump could not open file {:?}",
                filepath.as_os_str()
            );
            println!(
                "SeqSketcher dump: could not open file {:?}",
                filepath.as_os_str()
            );
            return Err("SeqSketcher dump failed".to_string());
        }
        //
        let mut writer = BufWriter::new(fileres.unwrap());
        to_writer(&mut writer, &self).unwrap();
        //
        Ok(())
    } // end of dump

    /// reload from a json dump
    pub fn reload_json(dirpath: &Path) -> Result<SeqSketcherParams, String> {
        log::info!("in reload_json");
        //
        let filepath = dirpath.join("sketchparams_dump.json");
        let fileres = OpenOptions::new().read(true).open(&filepath);
        if fileres.is_err() {
            log::error!(
                "Sketcher reload_json : reload could not open file {:?}",
                filepath.as_os_str()
            );
            println!(
                "Sketcher reload_json: could not open file {:?}",
                filepath.as_os_str()
            );
            return Err("Sketcher reload_json could not open file".to_string());
        }
        //
        let loadfile = fileres.unwrap();
        let reader = BufReader::new(loadfile);
        let sketch_params: SeqSketcherParams = serde_json::from_reader(reader).unwrap();
        //
        log::info!(
            "SeqSketcher reload, kmer_size : {}, sketch_size : {}",
            sketch_params.get_kmer_size(),
            sketch_params.get_sketch_size()
        );
        //
        Ok(sketch_params)
    } // end of reload_json
} // end of SeqSketcherParams

//==========================================================================================