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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,134 @@ | ||
| pub mod cli; | ||
| #![feature(trait_upcasting)] | ||
|
|
||
| use astarpa::{make_aligner, HeuristicParams}; | ||
| use astarpa2::AstarPa2Params; | ||
| use bio::io::fasta; | ||
| use clap::{value_parser, Parser}; | ||
| use itertools::Itertools; | ||
| use pa_types::{Aligner, Seq}; | ||
| use rand::{Rng, SeedableRng}; | ||
| use rand_chacha::ChaCha8Rng; | ||
| use serde::{Deserialize, Serialize}; | ||
| use std::{ | ||
| fs::File, | ||
| io::{BufRead, BufReader}, | ||
| ops::ControlFlow, | ||
| path::PathBuf, | ||
| }; | ||
|
|
||
| #[derive(clap::ValueEnum, Default, Debug, Clone, Copy, Serialize, Deserialize, PartialEq, Eq)] | ||
| pub enum AlignerType { | ||
| Astarpa, | ||
| Astarpa2Simple, | ||
| #[default] | ||
| Astarpa2Full, | ||
| } | ||
|
|
||
| impl AlignerType { | ||
| pub fn build(&self) -> Box<dyn Aligner> { | ||
| match self { | ||
| AlignerType::Astarpa => make_aligner(true, &HeuristicParams::default()), | ||
| AlignerType::Astarpa2Simple => AstarPa2Params::simple().make_aligner(true), | ||
| AlignerType::Astarpa2Full => AstarPa2Params::full().make_aligner(true), | ||
| } | ||
| } | ||
| } | ||
|
|
||
| /// Globally align pairs of sequences using A*PA. | ||
| #[derive(Parser, Serialize, Deserialize)] | ||
| #[clap(author, about, disable_version_flag(true))] | ||
| // Override some generator flags | ||
| #[clap(mut_arg("seed", |a| a.hide_short_help(true)))] | ||
| #[clap(mut_arg("cnt", |a| a.hide_short_help(true)))] | ||
| #[clap(mut_arg("size", |a| a.hide_short_help(true)))] | ||
| #[clap(mut_arg("error_model", |a| a.hide_short_help(true)))] | ||
| #[clap(mut_arg("error_model", |a| a.hide_short_help(true)))] | ||
| #[clap(group( | ||
| clap::ArgGroup::new("input_type") | ||
| .required(true) | ||
| .args(&["input", "length"]), | ||
| ))] | ||
| pub struct Cli { | ||
| /// A .seq, .txt, or Fasta file with sequence pairs to align. | ||
| #[clap(short, long, value_parser = value_parser!(PathBuf), display_order = 1)] | ||
| pub input: Option<PathBuf>, | ||
|
|
||
| /// Write a .csv of `{cost},{cigar}` lines | ||
| #[clap(short, long, value_parser = value_parser!(PathBuf), display_order = 1)] | ||
| pub output: Option<PathBuf>, | ||
|
|
||
| /// The aligner to use. | ||
| #[clap(long, default_value = "astarpa2-full")] | ||
| pub aligner: AlignerType, | ||
|
|
||
| /// Options to generate an input pair. | ||
| #[clap(flatten, next_help_heading = "Generated input")] | ||
| pub generate: pa_generate::DatasetGenerator, | ||
| } | ||
|
|
||
| impl Cli { | ||
| /// Call the given function for each pair in the input. | ||
| pub fn process_input_pairs(&self, mut run_pair: impl FnMut(Seq, Seq) -> ControlFlow<()>) { | ||
| if let Some(input) = &self.input { | ||
| // Parse file | ||
| let files = if input.is_file() { | ||
| vec![input.clone()] | ||
| } else { | ||
| input | ||
| .read_dir() | ||
| .expect(&format!("{} is not a file or directory", input.display())) | ||
| .map(|x| x.unwrap().path()) | ||
| .collect_vec() | ||
| }; | ||
|
|
||
| 'outer: for f in files { | ||
| match f.extension().expect("Unknown file extension") { | ||
| ext if ext == "seq" || ext == "txt" => { | ||
| let f = std::fs::File::open(&f).unwrap(); | ||
| let f = BufReader::new(f); | ||
| for (mut a, mut b) in f.lines().map(|l| l.unwrap().into_bytes()).tuples() { | ||
| if ext == "seq" { | ||
| assert_eq!(a.remove(0), '>' as u8); | ||
| assert_eq!(b.remove(0), '<' as u8); | ||
| } | ||
| if let ControlFlow::Break(()) = run_pair(&a, &b) { | ||
| break 'outer; | ||
| } | ||
| } | ||
| } | ||
| ext if ext == "fna" || ext == "fa" || ext == "fasta" => { | ||
| for (a, b) in fasta::Reader::new(BufReader::new(File::open(&f).unwrap())) | ||
| .records() | ||
| .tuples() | ||
| { | ||
| if let ControlFlow::Break(()) = | ||
| run_pair(a.unwrap().seq(), b.unwrap().seq()) | ||
| { | ||
| break 'outer; | ||
| } | ||
| } | ||
| } | ||
| ext => { | ||
| unreachable!( | ||
| "Unknown file extension {ext:?}. Must be in {{seq,txt,fna,fa,fasta}}." | ||
| ) | ||
| } | ||
| }; | ||
| } | ||
| } else { | ||
| // Generate random input. | ||
| let seed = self.generate.seed.unwrap_or_else(|| { | ||
| let seed = ChaCha8Rng::from_entropy().gen_range(0..1_000); | ||
| eprintln!("Seed: {seed}"); | ||
| seed | ||
| }); | ||
| let ref mut rng = ChaCha8Rng::seed_from_u64(seed); | ||
| for _ in 0..self.generate.cnt.unwrap() { | ||
| let (a, b) = self.generate.settings.generate(rng); | ||
| if let ControlFlow::Break(()) = run_pair(&a, &b) { | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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