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@@ -990,6 +990,7 @@ pub fn dot_graph_biall(
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#[cfg(test)]
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mod tests {
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+ use env_logger::Env;
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use dashmap::DashSet;
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use indicatif::MultiProgress;
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@@ -1002,6 +1003,12 @@ mod tests {
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phase::{merge_phases, variants_phasing, write_phases_bed, HeteroVar, Phase},
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};
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+ fn init() {
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+ let _ = env_logger::Builder::from_env(Env::default().default_filter_or("info"))
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+ .is_test(true)
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+ .try_init();
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+ }
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+
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#[test]
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fn it_works() -> Result<()> {
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let _ = env_logger::builder().is_test(true).try_init();
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@@ -1030,16 +1037,23 @@ mod tests {
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#[test]
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fn test_graph() -> Result<()> {
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- let chrom = vec!["chr9", "chr11"];
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- let dir = "/data/longreads_basic_pipe/ROBIN/diag/neo_contigs";
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+ init();
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+
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+ let case = "MERY";
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+ let chrom = vec!["chr7"];
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+ info!("This record will be captured by `cargo test`");
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+
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+ let dir = format!("/data/longreads_basic_pipe/{case}/diag/neo_contigs");
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// Load from fasta in dir.
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- let genome = Genome::from_contigs_sequences(dir)?;
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+ let genome = Genome::from_contigs_sequences(&dir)?;
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+ genome.stats();
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let mut genomic_graph = GenomicGraph::from_genome(&genome);
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let sens = vec![true, false];
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let pos = vec![0, i32::MAX];
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let mut all_ways = Vec::new();
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+ if chrom.len() > 1 {
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(0..4).into_iter().for_each(|i| {
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let start_pos = if i < 2 { 0 } else { i32::MAX };
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let end_pos = pos[i % 2];
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@@ -1047,27 +1061,49 @@ mod tests {
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(0..4).into_iter().for_each(|i| {
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let start_sens = if i < 2 { true } else { false };
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let end_sens = sens[i % 2];
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-
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- (0..4).into_iter().for_each(|i| {
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- let start_chr = if i < 2 { chrom[0] } else { chrom[1] };
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- let end_chr = chrom[i % 2];
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- let start = (start_sens, start_chr, start_pos);
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- let end = (end_sens, end_chr, end_pos);
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-
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- let (_oriented_graph, _integrated_graph, ways) = genomic_graph.ways(start, end);
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- // let dot = oriented_graph.dot_graph();
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-
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- for (_i, way) in ways.iter().enumerate() {
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- let s = way
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- .iter()
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- .map(|(_, _, _, s)| s.to_string())
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- .collect::<Vec<String>>()
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- .join("");
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- all_ways.push(s);
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- }
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- });
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+ (0..4).into_iter().for_each(|i| {
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+ let start_chr = if i < 2 { chrom[0] } else { chrom[1] };
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+ let end_chr = chrom[i % 2];
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+ let start = (start_sens, start_chr, start_pos);
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+ let end = (end_sens, end_chr, end_pos);
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+
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+ let (oriented_graph, _integrated_graph, ways) =
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+ genomic_graph.ways(start, end);
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+
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+ let dot = oriented_graph.dot_graph();
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+ println!("dot\n{dot}");
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+
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+ for (_i, way) in ways.iter().enumerate() {
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+ let s = way
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+ .iter()
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+ .map(|(_, _, _, s)| s.to_string())
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+ .collect::<Vec<String>>()
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+ .join("");
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+ all_ways.push(s);
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+ }
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+ });
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});
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});
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+ } else {
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+ let start_chr = chrom[0];
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+ let end_chr = chrom[0];
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+ let start = (true, start_chr, 0);
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+ let end = (true, end_chr, i32::MAX);
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+
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+ let (oriented_graph, _integrated_graph, ways) = genomic_graph.ways(start, end);
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+
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+ let dot = oriented_graph.dot_graph();
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+ println!("dot\n{dot}");
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+
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+ for (_i, way) in ways.iter().enumerate() {
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+ let s = way
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+ .iter()
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+ .map(|(_, _, _, s)| s.to_string())
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+ .collect::<Vec<String>>()
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+ .join("");
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+ all_ways.push(s);
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+ }
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+ }
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all_ways.dedup();
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all_ways
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