How to read a FASTA file

Drashti Shah

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Bioinformatics with Rust

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2 min read

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Dec 7, 2023

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A Rust function that returns a HashMap containing sequence IDs or headers as keys and DNA sequences as values extracted from a FASTA file

Arguments

• file_path: a string slice that holds path to the text file (in FASTA format)

Example

>Header_000
ACTG
>Header_001
AAAT

// Assume the text file above is named "sample_file.fa"
let data = read_fasta("sample_file.fa");

// data holds
// {"Header_001": "AAAT", "Header_000": "ACTG"}

Code

use std::collections::HashMap;
use std::fs::File;
use std::io::{BufRead, BufReader};

fn read_fasta(file_path: &str) -> HashMap<String, String> {
    let mut data = HashMap::new();
    let file = File::open(file_path).expect("Invalid filepath");
    let reader = BufReader::new(file);
    
    let mut seq_id = String::new();

    for line in reader.lines() {
        let line = line.unwrap();
        
        // Check if the line starts with '>' (indicating a sequence ID or header)
        if line.starts_with('>') {
            seq_id = line.trim_start_matches('>').to_string();
        } else {
            // If it's a DNA sequence line, insert or update the HashMap entry
            // If seq_id is not present, insert a new entry with an empty String
            // Then append the current line to the existing DNA sequence
            data.entry(seq_id.clone()).or_insert_with(String::new).push_str(&line);
        }
    }
    
    data
}

Some notes on the code

• trim_start_matches('>') removes all > from the start of seq_id
• It seems like BufRead is not used anywhere, but reader.lines() needs this trait in scope to create an iterator
• Note that you can only push a &str to an existing String (you can’t append/concatenate a String with another String)
• data.entry() will take ownership of seq_id and make it invalid if we don’t clone it

Next Steps

• You can set up Rust in your JupyterLab environment with this article
• You can download the Jupyter notebook for this post and play with the code
• You can download the sample FASTA file too