generated from mschoi/template
Myeongseon Choi
b25ed7e13d
- Introduced `prob700`, `prob808`, and `prob816` modules for new problem implementations in the Project Euler series. - Added utility functions for calculating Euler coins and their sums, as well as methods for finding reversible primes and calculating shortest distances in a modular context. - Updated the `mod.rs` files to include the new problem modules in both the Project Euler and Rosalind sections. - Enhanced the `integer` and `modulo` utility modules with new functions for coprimality checks and modular multiplication. - Included unit tests for the new functionalities to ensure correctness and reliability. - Refactored existing tests for consistency in the `finding_protein_motif` module.
93 lines
3.0 KiB
Rust
93 lines
3.0 KiB
Rust
use crate::utils::biology::{motif::Motif, uniprot::get_sequence_from_uniprot};
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use std::thread::sleep;
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use std::time::Duration;
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pub fn find_protein_motif(protein: &str, motif: &str) -> Vec<usize> {
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let motif = Motif::from_str(motif).unwrap();
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motif
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.find_matches(protein)
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.into_iter()
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.map(|p| p + 1)
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.collect()
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}
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pub fn find_protein_motif_in_uniprot(uniprot_id: &str, motif: &str) -> Vec<usize> {
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let sequence = get_sequence_from_uniprot(uniprot_id).unwrap();
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println!("{}", sequence);
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find_protein_motif(&sequence, motif)
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}
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pub fn find_protein_motif_in_uniprot_list(inputs: &str, motif: &str) -> String {
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let mut result = Vec::new();
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for input in inputs.split(" ") {
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let uniprot_id = input.split("_").next().unwrap();
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let positions = find_protein_motif_in_uniprot(uniprot_id, motif);
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if !positions.is_empty() {
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result.push(format!(
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"{}\n{}",
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input,
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positions
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.iter()
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.map(|p| p.to_string())
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.collect::<Vec<String>>()
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.join(" ")
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));
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}
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sleep(Duration::from_millis(10));
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}
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result.join("\n")
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}
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#[cfg(test)]
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mod tests {
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use super::*;
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#[test]
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fn test_find_protein_motif() {
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let protein = "MRASRPVVHPVEAPPPAALAVAAAAVAVEAGVGAGGGAAAHGGENAQPRGVRMKDPPGAPGTPGGLGLRLVQAFFAAAALAVMASTDDFPSVSAFCYLVAAAILQCLWSLSLAVVDIYALLVKRSLRNPQAVCIFTIGDGITGTLTLGAACASAGITVLIGNDLNICANNHCASFETATAMAFISWFALAPSCVLNFWSMASR";
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let motif = "N{P}[ST]{P}";
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let positions = find_protein_motif(protein, motif);
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assert_eq!(positions, Vec::<usize>::new());
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let protein = "GCATGATACATG";
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let motif = "CAT";
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let positions = find_protein_motif(protein, motif);
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assert_eq!(positions, vec![2, 9]);
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let protein = "AAAAA";
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let motif = "AA";
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let positions = find_protein_motif(protein, motif);
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assert_eq!(positions, vec![1, 2, 3, 4]);
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}
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#[test]
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fn test_find_protein_motif_in_uniprot() {
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let motif = "N{P}[ST]{P}";
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let uniprot_id = "A2Z669";
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let positions = find_protein_motif_in_uniprot(uniprot_id, motif);
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assert_eq!(positions, Vec::<usize>::new());
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sleep(Duration::from_millis(10));
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let uniprot_id = "B5ZC00";
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let positions = find_protein_motif_in_uniprot(uniprot_id, motif);
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assert_eq!(positions, vec![85, 118, 142, 306, 395]);
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sleep(Duration::from_millis(10));
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let uniprot_id = "P07204";
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let positions = find_protein_motif_in_uniprot(uniprot_id, motif);
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assert_eq!(positions, vec![47, 115, 116, 382, 409]);
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sleep(Duration::from_millis(10));
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let uniprot_id = "P20840";
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let positions = find_protein_motif_in_uniprot(uniprot_id, motif);
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assert_eq!(
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positions,
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vec![79, 109, 135, 248, 306, 348, 364, 402, 485, 501, 614]
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);
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}
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}
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