gc_count.rs

//based off https://gist.github.com/samuell/5555803
use std::fs::File;
use std::io::BufReader;
use std::io::prelude::*;
use std::env;

fn main() {
    let mut file = BufReader::new(File::open("Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa"));
    let content = gc_content(&mut file);
    println!("{:.2}", content * 100.0);
}

fn gc_content<R: BufRead>(reader: &mut R) -> f32 {
    let mut gc_count = 0u32;
    let mut at_count = 0u32;
    let mut line = Vec::with_capacity(1000);
    loop {
        reader.read_until(b'\n', &mut line).unwrap();
        
        if line.len() == 0 { break; }

        if line[0] == b'>' { line.clear(); continue; }

        for &byte in &line {
            match byte {
                b'G' | b'C' => gc_count += 1,
                b'A' | b'T' => at_count += 1,
                _ => {},
            }
        }

        line.clear();
    }
    gc_count as f32 / (gc_count as f32 + at_count as f32)
}