gff转化成bed文件 rust代码实现

use std::env;
use colored::Colorize;

fn help() {
    println!("
{} {}  {}  {}
2023/01/19
",  format!("usage: gff2bed").yellow(),
    format!("gene/mRNA").blue(),
    format!("ID/Name").green(),
    format!("gff_file").cyan());
}

#[warn(unused_variables)]
fn main() -> std::io::Result<()> {
    let args:Vec<String> = env::args().collect();
    if args.len() == 1 {
        help();
    }
    if args.len() != 4 {
        help();
        return Ok(());
    }
    let gene = &args[1];
    let id = &args[2];
    let file = &args[3];


    let mut reader = my_reader::BufReader::open(file)?;
    let mut buffer = String::new();

    while let Some(line) = reader.read_line(&mut buffer) {
        let line = line?;
        line_transform(line,id,gene);

        
    }

    Ok(())
}
fn line_transform(line:& mut String,id:&String,gene:&String)  -> i32{
    let a = id;
    let a_l:Vec<&str> = line.split('\t').collect();
    if a_l[0].starts_with('#'){
        return 0;
    }
    // print!("{:?}",a_l);
    let chr = a_l[0];
    let start = a_l[3];
    let end = a_l[4];
    let direction = a_l[6];
    if a_l[2] == gene {
        let ll = a_l[8].split(';').collect::<Vec<&str>>();
        let id = ll.iter().position(| &x|x.starts_with(a)).expect("get id error");
        let mut aa = a.to_string();
        aa.push('=');
        println!("{}\t{}\t{}\t{}\t{}\t{}",chr,start,end,ll[id].trim_start_matches(&aa).trim_end_matches('\n'),'0',direction);
        return  1;
    }
    return  0;




}
mod my_reader {
    use std::{
        fs::File,
        io::{self, prelude::*},
    };

    pub struct BufReader {
        reader: io::BufReader<File>,
    }

    impl BufReader {
        pub fn open(path: impl AsRef<std::path::Path>) -> io::Result<Self> {
            let file = File::open(path)?;
            let reader = io::BufReader::new(file);

            Ok(Self { reader })
        }

        pub fn read_line<'buf>(
            &mut self,
            buffer: &'buf mut String,
        ) -> Option<io::Result<&'buf mut String>> {
            buffer.clear();

            self.reader
                .read_line(buffer)
                .map(|u| if u == 0 { None } else { Some(buffer) })
                .transpose()
        }
    }
}

前一段时间一直在折腾rust语言，这语言太难了，只能刷刷力扣题目，然后在平时的生信项目中多使用rust解决工具。