Rust tagfinder
This commit is contained in:
parent
53f6a60943
commit
13f872cf10
GPG Key ID:
9B02406F8C4FB765
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# This file is automatically @generated by Cargo.
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# It is not intended for manual editing.
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"windows-targets",
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dependencies = [
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"windows_aarch64_gnullvm",
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"windows_aarch64_msvc",
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"windows_i686_gnu",
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"windows_i686_gnullvm",
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"windows_i686_msvc",
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"windows_x86_64_gnu",
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"windows_x86_64_gnullvm",
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"windows_x86_64_msvc",
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]
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[[package]]
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[[package]]
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[[package]]
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name = "windows_x86_64_gnullvm"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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[[package]]
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name = "windows_x86_64_msvc"
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version = "0.52.6"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||||
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@ -0,0 +1,7 @@
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[package]
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name = "tagfinder"
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version = "0.1.0"
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edition = "2021"
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[dependencies]
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clap = { version = "4.5.20", features = ["derive"] }
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@ -0,0 +1,2 @@
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run:
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cargo run -- --families test/samples/families.tsv --positions test/samples/position.tsv --definitions 0,1
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@ -0,0 +1,135 @@
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use std::cmp::Ordering;
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use std::collections::HashMap;
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use std::fs::File;
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use std::io::{self, BufRead};
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use std::path::Path;
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fn read_lines<P>(filename: P) -> io::Result<io::Lines<io::BufReader<File>>>
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where
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P: AsRef<Path>,
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{
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let file = File::open(filename)?;
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Ok(io::BufReader::new(file).lines())
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}
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pub fn parse_families<P>(filename: P) -> HashMap<String, u64>
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where
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P: AsRef<Path>,
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{
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let mut map: HashMap<String, u64> = HashMap::new();
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if let Ok(lines) = read_lines(filename) {
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for line in lines.flatten() {
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let parts: Vec<&str> = line.split("\t").collect();
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let gene = parts[0];
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let family: u64 = parts[1].parse().unwrap();
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map.insert(gene.to_string(), family);
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}
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}
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map
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}
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pub fn parse_position<P>(filename: P) -> Vec<(String, String, u64, u64)>
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where
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P: AsRef<Path>,
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{
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let mut vec: Vec<(String, String, u64, u64)> = Vec::new();
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if let Ok(lines) = read_lines(filename) {
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for line in lines.flatten() {
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let parts: Vec<&str> = line.split("\t").collect();
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let gene = parts[0];
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let chromosome = parts[1];
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let start: u64 = parts[2].parse().unwrap();
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let end: u64 = parts[3].parse().unwrap();
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vec.push((gene.to_string(), chromosome.to_string(), start, end));
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}
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}
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vec
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}
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pub fn compare_gene_position(
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position_a: &(String, String, u64, u64),
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position_b: &(String, String, u64, u64),
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) -> Ordering {
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let (_gene_a, chromosome_a, start_a, _end_b) = position_a;
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let (_gene_b, chromosome_b, start_b, _end_b) = position_b;
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if chromosome_a < chromosome_b {
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return Ordering::Less;
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} else if chromosome_a > chromosome_b {
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return Ordering::Greater;
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} else {
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if start_a < start_b {
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return Ordering::Less;
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} else {
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return Ordering::Greater;
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}
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}
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}
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pub fn detect_tag_of_definitions(
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definitions: &Vec<u64>,
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gene_positions: &Vec<(String, String, u64, u64)>,
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gene_families: &HashMap<String, u64>,
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) -> HashMap<String, (String, Vec<Option<u64>>)> {
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let mut tag_numbers: HashMap<String, (String, Vec<Option<u64>>)> = HashMap::new();
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for definition in definitions {
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let tag_numbers_def = detect_tag_of_definition(*definition, gene_positions, gene_families);
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for (gene, (family, tag)) in tag_numbers_def {
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if tag_numbers.contains_key(&gene) {
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let (_gene, tags) = tag_numbers.get_mut(&gene).unwrap();
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tags.push(tag);
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} else {
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tag_numbers.insert(gene, (family, vec![tag]));
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}
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}
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}
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tag_numbers
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}
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pub fn detect_tag_of_definition(
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definition: u64,
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gene_positions: &Vec<(String, String, u64, u64)>,
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gene_families: &HashMap<String, u64>,
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) -> HashMap<String, (String, Option<u64>)> {
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let mut tag_numbers: HashMap<String, (String, Option<u64>)> = HashMap::new();
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let mut spacer_index: u64 = 0;
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let mut tag_index: u64 = 0;
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||||||
|
for (i, (gene_i, chromosome_i, _start_i, _end_i)) in gene_positions.iter().enumerate() {
|
||||||
|
let family_repr: String;
|
||||||
|
let mut is_on_tag: bool = false;
|
||||||
|
if let Some(family_i) = gene_families.get(gene_i) {
|
||||||
|
family_repr = format!("{}", family_i);
|
||||||
|
let mut nb_intra_tag_spacers: u64 = 0;
|
||||||
|
if !tag_numbers.contains_key(gene_i) {
|
||||||
|
for (gene_j, chromosome_j, _start_j, _end_j) in &gene_positions[(i + 1)..] {
|
||||||
|
if *chromosome_i != *chromosome_j {
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
if let Some(family_j) = gene_families.get(gene_j) {
|
||||||
|
if *family_i == *family_j {
|
||||||
|
nb_intra_tag_spacers = 0;
|
||||||
|
if !is_on_tag {
|
||||||
|
is_on_tag = true;
|
||||||
|
tag_index += 1;
|
||||||
|
tag_numbers.insert(gene_i.clone(), (family_repr.clone(), Some(tag_index)));
|
||||||
|
}
|
||||||
|
tag_numbers.insert(gene_j.clone(), (family_repr.clone(), Some(tag_index)));
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
nb_intra_tag_spacers += 1;
|
||||||
|
}
|
||||||
|
if nb_intra_tag_spacers > definition {
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if !is_on_tag {
|
||||||
|
tag_numbers.insert(gene_i.clone(), (family_repr, None));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
spacer_index += 1;
|
||||||
|
family_repr = format!("spacer{}", spacer_index);
|
||||||
|
tag_numbers.insert(gene_i.clone(), (family_repr, None));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
tag_numbers
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,57 @@
|
||||||
|
use std::{collections::HashMap, path::PathBuf};
|
||||||
|
use clap::Parser;
|
||||||
|
use finder::{detect_tag_of_definitions, parse_families, parse_position};
|
||||||
|
|
||||||
|
mod finder;
|
||||||
|
|
||||||
|
#[derive(Parser)]
|
||||||
|
#[command(version="0.0.1", about="Find Tandemly Arrayed Genes", long_about="Find Tandemly Arrayed Genes in a genome based on gene position and Tandemly Arrayed Genes definition (i. e. number of spacers)")]
|
||||||
|
struct Cli {
|
||||||
|
#[arg(short='f', long="families", value_name="FAMILIES FILE")]
|
||||||
|
families: PathBuf,
|
||||||
|
|
||||||
|
#[arg(short='p', long="positions", value_name="POSITIONS FILE")]
|
||||||
|
positions: PathBuf,
|
||||||
|
|
||||||
|
#[arg(short='d', long="definitions", value_name="TAGs DEFINITIONS", help="Comma seperated integers for the number of spacers to consider")]
|
||||||
|
definitions: String
|
||||||
|
}
|
||||||
|
|
||||||
|
fn main() {
|
||||||
|
let cli = Cli::parse();
|
||||||
|
|
||||||
|
let gene_families: HashMap<String, u64> = parse_families(cli.families);
|
||||||
|
|
||||||
|
let mut gene_positions: Vec<(String, String, u64, u64)> = parse_position(cli.positions);
|
||||||
|
|
||||||
|
gene_positions.sort_by(|a, b | crate::finder::compare_gene_position(a, b));
|
||||||
|
|
||||||
|
let definitions: Vec<u64> = cli.definitions.split(",").map(|x| x.parse().unwrap()).collect();
|
||||||
|
|
||||||
|
let tag_numbers = detect_tag_of_definitions(&definitions, &gene_positions, &gene_families);
|
||||||
|
|
||||||
|
// Print header
|
||||||
|
print!("gene\tfamily\t");
|
||||||
|
for (i, definition) in definitions.iter().enumerate() {
|
||||||
|
print!("tag{}", definition);
|
||||||
|
if (i + 1) < definitions.len() {
|
||||||
|
print!("\t");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
print!("\n");
|
||||||
|
|
||||||
|
for (gene, (family, tags)) in tag_numbers {
|
||||||
|
print!("{}\t{}\t", gene, family);
|
||||||
|
for (i, tag) in tags.iter().enumerate() {
|
||||||
|
if let Some(tag) = tag {
|
||||||
|
print!("{}", tag);
|
||||||
|
} else {
|
||||||
|
print!("-");
|
||||||
|
}
|
||||||
|
if (i + 1) < tags.len() {
|
||||||
|
print!("\t");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
print!("\n");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,4 @@
|
||||||
|
A 1
|
||||||
|
B 1
|
||||||
|
C 2
|
||||||
|
D 2
|
||||||
|
|
|
@ -0,0 +1,6 @@
|
||||||
|
A 1 1 1
|
||||||
|
B 1 2 1
|
||||||
|
C 2 3 1
|
||||||
|
U 2 4 1
|
||||||
|
V 2 5 1
|
||||||
|
D 2 10 1
|
||||||
|
Loading…
Reference in New Issue