gfa-reader 0.1.4

Reading gfa format v1
Documentation 
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use gfa_reader::{Link, Gfa, NCGfa, Pansn, Path};

#[test]
/// Check full header
fn read_gfa_header() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, false);
    assert_eq!(graph.header.version_number, "1.0".to_string());
    assert_eq!(graph.header.tag, "VN".to_string());
    assert_eq!(graph.header.typ, "Z".to_string());

}


#[test]
fn read_gfa_edges() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, true);
    assert_eq!(&graph.links.as_ref().unwrap().len(), &35381);
    assert_eq!(&graph.links.clone().unwrap()[0],
               &Link { from: "1".to_string(), from_dir: true, to_dir: true, to: "78".to_string(), overlap: "0M".to_string(), opt: () });

    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, false);
    assert_eq!(graph.links, None);
}


#[test]
fn read_gfa_nodes() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, false);
    assert_eq!(graph.segments[9].opt, ());
    assert_eq!(graph.segments.len(), 26234);
    assert_eq!(graph.paths[0].nodes[0], "4".to_string());
}


#[test]
fn read_gfa_nodes2() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, false);
    let gra: Pansn<Path> = Pansn::from_graph(&graph.paths, " ");
    assert_eq!(gra.genomes.len(), 5);
}

#[test]
fn read_gfa_convert_nodes() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: NCGfa<()> = NCGfa::new();
    graph.parse_gfa_file_direct(filename, false);
    assert_eq!(graph.nodes[9].opt, ());
    assert_eq!(graph.nodes[1-1].id, 1);
    if graph.mapper.len() != graph.nodes.len() {
        graph.mapper = graph.nodes.iter().map(| x| x.id.to_string()).collect();
    }
    assert_eq!(graph.get_old_node(&1),  &1.to_string());
    assert_eq!(graph.nodes.len(), 26234);
    assert_eq!(graph.nodes[0].id, 1);
    assert_eq!(graph.paths[0].nodes[0], 4);


}




#[test]
fn read_gfa_convert_nodes2() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: NCGfa<()> = NCGfa::new();
    graph.parse_gfa_file_and_convert(filename, false);
    assert_eq!(graph.nodes[9].opt, ());
    assert_eq!(graph.nodes[1-1].id, 1);
    assert_eq!(graph.nodes.len(), 26234);
    assert_eq!(graph.nodes[0].id, 1);
    assert_eq!(graph.paths[0].nodes[0], 4);
    assert_eq!(graph.mapper.len(), 26234);


}



#[test]
fn read_ncgfa_nodes() {
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: NCGfa<()> = NCGfa::new();
    graph.parse_gfa_file_direct(filename, false);
    assert_eq!(graph.nodes[9].opt, ());
    assert_eq!(graph.nodes[1-1].id, 1);
}

#[test]
fn convert_gfa_ncgfa(){
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, false);
    let a = graph.convert_to_ncgraph(&graph);
    assert_eq!(graph.segments[1].sequence, a.nodes[1].seq);
    assert_eq!(graph.segments[1].opt, a.nodes[1].opt);
    assert_eq!(graph.segments[1].name, a.nodes[1].id.to_string());
    assert_eq!(a.nodes[1].id, 2)
}


#[test]
fn convert_gfa_ncgfa2(){
    eprintln!("Read gfa");
    // Example data
    let filename = "data/size5.gfa";
    let mut graph: Gfa<()> = Gfa::new();
    graph.parse_gfa_file(filename, false);
    let a = graph.convert_to_ncgraph(&graph);
    assert_eq!(true, a.check_numeric());
}