Starting to learn Rust

Trimming UMI

Aurélien Ginolhac


August 17, 2023


I am very happy with but I want to learn something new, another programming language. The desire comes with several needs

Opposite of R:

  • A compiled language
    • Speed
    • Strict syntax, almost pedantic
  • Strongly typed

Similarities to R:

  • Full of functional programming
  • Great packages offered by a great community (crates)

Turns out this language is Rust.



It is incredibly helpful. I am using VScode with the extension rust-analyser that provides immediate feedback, great suggestions to both warnings and errors.

Learning material

I am using so far three resources:

Example of syntax

Programs are managed by the cargo utility. It creates, run, test, optimize Rust code. Here is one of official documentation example. We need the rand crate dependency. Here we specify the wanted version 0.8.5.

The code for the main guessing is included.

name = "guessing_game"
version = "0.1.0"
edition = "2021"

# See more keys and their definitions at

rand = "0.8.5"
use std::io;
use std::cmp::Ordering;
use rand::Rng;

fn main() {
    println!("Guess the number!");
    let max = 50u32;
    // to keep track of the number of guesses
    let mut count = 0u32;

    // create an integer randomly from 1 to 50
    let secret_number = rand::thread_rng().gen_range(1..=max);
    // loop over until the number is found
    loop { 
        count += 1;   
        println!("Please input your guess. (an integer from 1 to {max})");
        let mut guess: String = String::new();
        .read_line(&mut guess)
        .expect("Failed to read line");
        // coerce to an integer
        let guess: u32 = match guess.trim().parse() {
            Ok(num) => num,
            // but offer possibily to change
            Err(_) => {
                println!("You entered {}, not a number", guess.trim());
        println!("You guessed: {guess}");  //while the secret was {secret_number}");
        match guess.cmp(&secret_number) {
            Ordering::Less => println!("Too small!"),
            Ordering::Greater => println!("Too big!"),
            Ordering::Equal => {
                println!("You win! in {count} trials");

First project: UMI trimming

UMI stands for Unique Molecular Identifier.

The goal is reproduce some features from umi-tools especially the extract command.

For example, convert the following read




The UMI was GTCAGT and appended to the read name, while being removed from the sequence along with the TATA linker.


This library rust-bio provides many features, and I am only using the

  • alphabets to check the letters are actually IUPAC / DNA
  • fastq for Reading/Writing FASTQ reads.

The Command Line Interface (CLI) utility: clap

clap is an awesome library that helps making a CLI fun and easy.

The help output looks like (options actually appear in bold:

$ umi_trim -h
Move Unique Molecular Identifier from seq to name and trim a linker motif (TATA)

Usage: umi_trim [OPTIONS] --input <INPUT> --output <OUTPUT>

  -i, --input <INPUT>            FASTQ filename to read from
  -o, --output <OUTPUT>          Filename to write to
  -u, --umi-length <UMI_LENGTH>  UMI length in characters [default: 6]
  -l, --linker <LINKER>          Linker UMI-READ to be discarded [default: TATA]
  -h, --help                     Print help
  -V, --version                  Print version

This project is here on