spqr-tree 5.1.0

A representation of the SPQR tree in Rust with support for I/O
Documentation 
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use std::{
    fs::{self, File},
    io::BufReader,
};

use bidirected_adjacency_array::{
    graph::BidirectedAdjacencyArray,
    io::gfa1::{PlainGfaEdgeData, PlainGfaNodeData},
};
use regex::Regex;

use crate::decomposition::SPQRDecomposition;

fn enable_logging() {
    let _ignore = simplelog::TermLogger::init(
        log::LevelFilter::Trace,
        Default::default(),
        simplelog::TerminalMode::Stdout,
        simplelog::ColorChoice::Auto,
    );
}

#[test]
fn test_tiny1() {
    enable_logging();
    let remove_edge_labels = Regex::new(r" E\d+ ").unwrap();

    let graph = BidirectedAdjacencyArray::<u8, PlainGfaNodeData, PlainGfaEdgeData>::read_gfa1(
        BufReader::new(File::open("test_files/tiny1.gfa").unwrap()),
    )
    .unwrap();
    let spqr_decomposition_file = fs::read_to_string("test_files/tiny1.spqr").unwrap();
    let spqr_decomposition =
        SPQRDecomposition::read_plain_spqr(&graph, &mut spqr_decomposition_file.as_bytes())
            .unwrap();

    let mut buffer = Vec::new();
    spqr_decomposition.write_plain_spqr(&mut buffer).unwrap();

    let spqr_decomposition_file = remove_edge_labels.replace_all(&spqr_decomposition_file, " E ");
    let mut spqr_decomposition_file_sorted = spqr_decomposition_file
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    spqr_decomposition_file_sorted.sort_unstable();
    let spqr_decomposition_file_sorted = spqr_decomposition_file_sorted;

    let buffer = std::str::from_utf8(&buffer).unwrap();
    let buffer = remove_edge_labels.replace_all(buffer, " E ");
    let mut buffer_sorted = buffer
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    buffer_sorted.sort_unstable();
    let buffer_sorted = buffer_sorted;

    assert_eq!(spqr_decomposition_file_sorted, buffer_sorted);
}

#[test]
fn test_random1_1_false_0() {
    enable_logging();
    let remove_edge_labels = Regex::new(r" E\d+ ").unwrap();

    let graph = BidirectedAdjacencyArray::<u8, PlainGfaNodeData, PlainGfaEdgeData>::read_gfa1(
        BufReader::new(File::open("test_files/random1_1_False_0.gfa").unwrap()),
    )
    .unwrap();
    let spqr_decomposition_file = fs::read_to_string("test_files/random1_1_False_0.spqr").unwrap();
    let spqr_decomposition =
        SPQRDecomposition::read_plain_spqr(&graph, &mut spqr_decomposition_file.as_bytes())
            .unwrap();

    let mut buffer = Vec::new();
    spqr_decomposition.write_plain_spqr(&mut buffer).unwrap();

    let spqr_decomposition_file = remove_edge_labels.replace_all(&spqr_decomposition_file, " E ");
    let mut spqr_decomposition_file_sorted = spqr_decomposition_file
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    spqr_decomposition_file_sorted.sort_unstable();
    let spqr_decomposition_file_sorted = spqr_decomposition_file_sorted;

    let buffer = std::str::from_utf8(&buffer).unwrap();
    let buffer = remove_edge_labels.replace_all(buffer, " E ");
    let mut buffer_sorted = buffer
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    buffer_sorted.sort_unstable();
    let buffer_sorted = buffer_sorted;

    assert_eq!(spqr_decomposition_file_sorted, buffer_sorted);
}

#[test]
fn test_multiedge() {
    enable_logging();
    let remove_edge_labels = Regex::new(r" E\d+ ").unwrap();

    let graph = BidirectedAdjacencyArray::<u8, PlainGfaNodeData, PlainGfaEdgeData>::read_gfa1(
        BufReader::new(File::open("test_files/multiedge.gfa").unwrap()),
    )
    .unwrap();
    let spqr_decomposition_file = fs::read_to_string("test_files/multiedge.spqr").unwrap();
    let spqr_decomposition =
        SPQRDecomposition::read_plain_spqr(&graph, &mut spqr_decomposition_file.as_bytes())
            .unwrap();

    let mut buffer = Vec::new();
    spqr_decomposition.write_plain_spqr(&mut buffer).unwrap();

    let spqr_decomposition_file = remove_edge_labels.replace_all(&spqr_decomposition_file, " E ");
    let mut spqr_decomposition_file_sorted = spqr_decomposition_file
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    spqr_decomposition_file_sorted.sort_unstable();
    let spqr_decomposition_file_sorted = spqr_decomposition_file_sorted;

    let buffer = std::str::from_utf8(&buffer).unwrap();
    let buffer = remove_edge_labels.replace_all(buffer, " E ");
    let mut buffer_sorted = buffer
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    buffer_sorted.sort_unstable();
    let buffer_sorted = buffer_sorted;

    assert_eq!(spqr_decomposition_file_sorted, buffer_sorted);
}

#[test]
fn test_random3_5_false_0() {
    enable_logging();
    let remove_edge_labels = Regex::new(r" E\d+ ").unwrap();

    let graph = BidirectedAdjacencyArray::<u8, PlainGfaNodeData, PlainGfaEdgeData>::read_gfa1(
        BufReader::new(File::open("test_files/random3_5_False_0.gfa").unwrap()),
    )
    .unwrap();
    let spqr_decomposition_file = fs::read_to_string("test_files/random3_5_False_0.spqr").unwrap();
    let spqr_decomposition =
        SPQRDecomposition::read_plain_spqr(&graph, &mut spqr_decomposition_file.as_bytes())
            .unwrap();

    let mut buffer = Vec::new();
    spqr_decomposition.write_plain_spqr(&mut buffer).unwrap();

    let spqr_decomposition_file = remove_edge_labels.replace_all(&spqr_decomposition_file, " E ");
    let mut spqr_decomposition_file_sorted = spqr_decomposition_file
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    spqr_decomposition_file_sorted.sort_unstable();
    let spqr_decomposition_file_sorted = spqr_decomposition_file_sorted;

    let buffer = std::str::from_utf8(&buffer).unwrap();
    let buffer = remove_edge_labels.replace_all(buffer, " E ");
    let mut buffer_sorted = buffer
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    buffer_sorted.sort_unstable();
    let buffer_sorted = buffer_sorted;

    assert_eq!(spqr_decomposition_file_sorted, buffer_sorted);
}

#[test]
fn test_random5_10_false_0() {
    enable_logging();
    let remove_edge_labels = Regex::new(r" E\d+ ").unwrap();

    let graph = BidirectedAdjacencyArray::<u8, PlainGfaNodeData, PlainGfaEdgeData>::read_gfa1(
        BufReader::new(File::open("test_files/random5_10_False_0.gfa").unwrap()),
    )
    .unwrap();
    let spqr_decomposition_file = fs::read_to_string("test_files/random5_10_False_0.spqr").unwrap();
    let spqr_decomposition =
        SPQRDecomposition::read_plain_spqr(&graph, &mut spqr_decomposition_file.as_bytes())
            .unwrap();

    let mut buffer = Vec::new();
    spqr_decomposition.write_plain_spqr(&mut buffer).unwrap();

    let spqr_decomposition_file = remove_edge_labels.replace_all(&spqr_decomposition_file, " E ");
    let mut spqr_decomposition_file_sorted = spqr_decomposition_file
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    spqr_decomposition_file_sorted.sort_unstable();
    let spqr_decomposition_file_sorted = spqr_decomposition_file_sorted;

    let buffer = std::str::from_utf8(&buffer).unwrap();
    let buffer = remove_edge_labels.replace_all(buffer, " E ");
    let mut buffer_sorted = buffer
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    buffer_sorted.sort_unstable();
    let buffer_sorted = buffer_sorted;

    assert_eq!(spqr_decomposition_file_sorted, buffer_sorted);
}

#[test]
fn test_ultrabubble_dataset_chr_22_g182870() {
    enable_logging();
    let remove_edge_labels = Regex::new(r" E\d+ ").unwrap();

    let graph = BidirectedAdjacencyArray::<u8, PlainGfaNodeData, PlainGfaEdgeData>::read_gfa1(
        BufReader::new(File::open("test_files/Ultrabubble_dataset_chr_22_G182870.gfa").unwrap()),
    )
    .unwrap();
    let spqr_decomposition_file =
        fs::read_to_string("test_files/Ultrabubble_dataset_chr_22_G182870.spqr").unwrap();
    let spqr_decomposition =
        SPQRDecomposition::read_plain_spqr(&graph, &mut spqr_decomposition_file.as_bytes())
            .unwrap();

    let mut buffer = Vec::new();
    spqr_decomposition.write_plain_spqr(&mut buffer).unwrap();

    let spqr_decomposition_file = remove_edge_labels.replace_all(&spqr_decomposition_file, " E ");
    let mut spqr_decomposition_file_sorted = spqr_decomposition_file
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    spqr_decomposition_file_sorted.sort_unstable();
    let spqr_decomposition_file_sorted = spqr_decomposition_file_sorted;

    let buffer = std::str::from_utf8(&buffer).unwrap();
    let buffer = remove_edge_labels.replace_all(buffer, " E ");
    let mut buffer_sorted = buffer
        .trim()
        .lines()
        .map(|line| line.trim())
        .collect::<Vec<_>>();
    buffer_sorted.sort_unstable();
    let buffer_sorted = buffer_sorted;

    assert_eq!(spqr_decomposition_file_sorted, buffer_sorted);
}