first commit

.gitignore

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+/target

Cargo.toml

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+[package]
+name = "krust"
+version = "0.1.0"
+edition = "2018"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+bio = "*"

Cargo.toml~

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+[package]
+name = "krust"
+version = "0.1.0"
+edition = "2018"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]

LICENSE

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+MIT License
+
+Copyright (c) 2021 suchapalaver
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+To make use of k-rust's multithreaded cocurrency test with the larger fasta data, which, be warned, is larger than github's recommended upload size. 
+
+Run k-rust on the test data, searching for kmers of length 5, like this:
+
+$ cargo run 5 cerevisae.pan_S288C_chrI.fa
+
+or, searching for kmers of length 21 across multiple records:
+
+$ cargo run 21 cerevisae.pan.fa

src/lib.rs

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+use std::{env, error::Error, fs::{self, File}, io::Write, path::Path, str, thread};
+
+extern crate bio;
+use bio::{alignment::sparse::hash_kmers, alphabets::dna::revcomp, io::fasta};
+
+pub struct Config {
+
+    pub kmer_len: String,
+    pub filepath: String,
+}
+
+impl Config {
+    pub fn new(mut args: env::Args) -> Result<Config, &'static str> {
+
+	args.next();
+
+        let kmer_len = match args.next() {
+
+            Some(arg) => arg,
+            None => return Err("Didn't get a k-mer length"),
+        };
+        let filepath = match args.next() {
+
+            Some(arg) => arg,
+            None => return Err("Didn't get a file name"),
+        };
+        Ok(Config {
+
+            kmer_len,
+            filepath,
+        })
+    }
+}
+
+pub fn run(config: Config) -> Result<(), Box<dyn Error>> {
+
+    fs::create_dir("output")?;
+
+    let filepath: String = config.filepath;
+
+    let kmer_len = config.kmer_len.parse::<usize>().unwrap();
+
+    let reader = fasta::Reader::from_file(&filepath).unwrap();
+
+    let mut threads = Vec::new();
+
+    for result in reader.records() {
+
+	let t = thread::spawn( move || {
+
+            let result_data = &result.unwrap();
+
+	    let pathname = format!("output/{}.tsv", result_data.id());
+
+	    let path = Path::new(&pathname);
+
+	    let display = path.display();
+
+	    let mut file = match File::create(&path) {
+
+		Err(why) => panic!("couldn't create {}: {}", display, why),
+		Ok(file) => file,
+	    };
+	    for (kmer, kmer_positions) in hash_kmers(result_data.seq(), kmer_len) {
+
+		//  trying to think about a better way to do
+		//  this than the nested match patterns below.
+		//  Here's immeidately below commented out is
+		//  one attempt that compiles but this is from
+		//  before I added print to file capability:		
+		/*
+		let kmer_s = str::from_utf8(&kmer).unwrap();
+		let rvc = revcomp(kmer);
+		let rvc_s = str::from_utf8(&rvc).unwrap();
+		println!("{}\t{}\t{}\t{}", result_data.id(), kmer_s, rvc_s, kmer_positions.len());
+	    }
+	    });
+		 */	
+		let rvc = revcomp(kmer);
+
+		match str::from_utf8(kmer) {
+
+		    Err(e) => println!("Problem: {}", e),    
+		    Ok(kmer_s) => {
+
+			match str::from_utf8(&rvc) {
+
+			    Ok(rvc) => {
+
+				let data = format!("{}\t{}\t{}\n", kmer_s, rvc, kmer_positions.len());
+				write!(file, "{}", data).expect("Unable to write file");
+			    }
+			    Err(why) => panic!("couldn't write to {}: {}", display, why),
+			}
+		    }
+		}
+	    }
+	});
+	threads.push(t);
+    }
+    for t in threads {
+
+	t.join().expect("thread failed");
+    }
+    Ok(println!("{}", filepath))
+}

src/main.rs

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+use std::env;
+use std::process;
+
+use krust::Config;
+
+fn main() {
+
+    let config = Config::new(env::args()).unwrap_or_else(|err| {
+        println!("Problem parsing arguments: {}", err);
+        process::exit(1);
+    });
+
+    println!("\nSearching for kmers of length {}", config.kmer_len);
+    println!("... in file {}\n", config.filepath);
+
+    if let Err(e) = krust::run(config) {
+        println!("Application error: {}", e);
+        process::exit(1);
+    }
+}   

src/main.rs~

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+fn main() {
+    println!("Hello, world!");
+}