sketchlib 0.4.1

Genome and amino-acid sketching
Documentation 
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use predicates::prelude::*;
use snapbox::cmd::{self, Command};
use std::path::Path;

pub mod common;
use crate::common::*;

use sketchlib::sketch::multisketch::MultiSketch;

#[cfg(test)]

mod tests {
    use super::*;

    #[test]
    fn test_concat_sketches() {
        let sandbox = TestSetup::setup();

        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("sketch")
            .args(&["--k-vals", "17"])
            .arg(sandbox.file_string("14412_3#82.contigs_velvet.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("14412_3#84.contigs_velvet.fa.gz", TestDir::Input))
            .arg("--quiet")
            .args(&["-o", "part1"])
            .assert()
            .success();

        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("sketch")
            .args(&["--k-vals", "17"])
            .arg(sandbox.file_string("R6.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("TIGR4.fa.gz", TestDir::Input))
            .arg("-v")
            .args(&["-o", "part2"])
            .assert()
            .success();

        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("sketch")
            .args(&["--k-vals", "17"])
            .arg(sandbox.file_string("R6.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("TIGR4.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("14412_3#82.contigs_velvet.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("14412_3#84.contigs_velvet.fa.gz", TestDir::Input))
            .arg("-v")
            .args(&["-o", "concat_ref"])
            .assert()
            .success();

        // Overlapping labels fails
        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("concat")
            .arg("part1")
            .arg(sandbox.file_string("14412_3#82.contigs_velvet.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("14412_3#84.contigs_velvet.fa.gz", TestDir::Input))
            .arg("-v")
            .args(&["-o", "concat_test"])
            .assert()
            .failure();

        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("append")
            .arg("part1")
            // .arg(sandbox.file_string("fasta_part2.txt", TestDir::Input))
            .arg(sandbox.file_string("R6.fa.gz", TestDir::Input))
            .arg(sandbox.file_string("TIGR4.fa.gz", TestDir::Input))
            .arg("-v")
            .args(&["-o", "concat_test"])
            .assert()
            .success();

        // Check .skm the same
        let concat_sketch: MultiSketch =
            MultiSketch::load_metadata(&sandbox.file_string("concat_test", TestDir::Output))
                .expect("Failed to load output merged sketch");
        let expected_sketch =
            MultiSketch::load_metadata(&sandbox.file_string("concat_ref", TestDir::Output))
                .expect("Failed to load expected merged sketch");
        println!("{}", concat_sketch);
        println!("{}", expected_sketch);
        assert_eq!(
            concat_sketch, expected_sketch,
            "Concat sketch metadata does not match"
        );

        // Check .skd the same
        let predicate_file = predicate::path::eq_file(Path::new(
            &sandbox.file_string("concat_test.skd", TestDir::Output),
        ));
        assert_eq!(
            true,
            predicate_file.eval(Path::new(
                &sandbox.file_string("concat_ref.skd", TestDir::Output)
            )),
            "Concat sketch data does not match"
        );
    }

    #[test]
    fn save_sketch_data_reexport_matches_utils() {
        let sandbox = TestSetup::setup();

        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("sketch")
            .args(&["--k-vals", "17"])
            .arg(sandbox.file_string("14412_3#82.contigs_velvet.fa.gz", TestDir::Input))
            .arg("--quiet")
            .args(&["-o", "reexport_part1"])
            .assert()
            .success();

        Command::new(cmd::cargo_bin!("sketchlib"))
            .current_dir(sandbox.get_wd())
            .arg("sketch")
            .args(&["--k-vals", "17"])
            .arg(sandbox.file_string("14412_3#84.contigs_velvet.fa.gz", TestDir::Input))
            .arg("--quiet")
            .args(&["-o", "reexport_part2"])
            .assert()
            .success();

        let part1 = sandbox.file_string("reexport_part1", TestDir::Output);
        let part2 = sandbox.file_string("reexport_part2", TestDir::Output);
        let via_reexport = sandbox.file_string("via_reexport", TestDir::Output);
        let via_utils = sandbox.file_string("via_utils", TestDir::Output);

        sketchlib::save_sketch_data(&part1, &part2, &via_reexport)
            .expect("save_sketch_data (re-export) failed");
        sketchlib::utils::save_sketch_data(&part1, &part2, &via_utils)
            .expect("utils::save_sketch_data failed");

        let predicate_file = predicate::path::eq_file(Path::new(&format!("{via_utils}.skd")));
        assert_eq!(
            true,
            predicate_file.eval(Path::new(&format!("{via_reexport}.skd"))),
            "Re-exported save_sketch_data output does not match utils::save_sketch_data"
        );
    }
}