https://github.com/alejandrogzi/noel

GTF/GFF per gene non-overlapping exon length calculator

https://github.com/alejandrogzi/noel

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GTF/GFF per gene non-overlapping exon length calculator

https://github.com/alejandrogzi/noel/blob/master/

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# noel

An extremely fast GTF/GFF per gene Non-Overlapping Exon Length calculator (noel) written in Rust.


    


Takes in a GTF/GFF file and outputs a .txt file with non-overlapping exon lengths. 

## Usage
``` rust
Usage: noel --i  --o 


Arguments:
    --i : GTF/GFF file
    --o 
: .txt file

Options:
    --help: print help
    --version: print version
```

#### crate: [https://crates.io/crates/noel](https://crates.io/crates/noel)


## Installation
to install noel on your system follow this steps:
1. download rust: `curl https://sh.rustup.rs -sSf | sh` on unix, or go [here](https://www.rust-lang.org/tools/install) for other options
2. run `cargo install noel` (make sure `~/.cargo/bin` is in your `$PATH` before running it)
4. use `noel` with the required arguments

## Build
to build noel from this repo, do:

1. get rust (as described above)
2. run `git clone https://github.com/alejandrogzi/noel.git && cd noel`
3. run `cargo run --release  
` (arguments are positional, so you do not need to specify --i/--o)

## Library
to include noel as a library and use it within your project follow these steps:
1. include `noel = 0.2.0` or `noel = "*"` under `[dependencies]` in your `Cargo.toml` file or just run `cargo add noel` from the command line
2. the library name is `noel`, to use it just write:

    ``` rust
    use noel::{noel, noel_reader}; 
    ```
    or 
    ``` rust
    use noel::*;
    ```
3. invoke
    ``` rust
    let exons: HashMap> = noel_reader(input: &PathBuf)?
    let lengths: Vec<(String, u32)> = noel(exons)
    ```
4. you will end with a HashMap, where each gene name (gene_id) is a key to its length
    ```text
    [("ENSG00000261469": 533), ("ENSG00000150990": 6908), ("ENSG00000136490": 4751), ("ENSG00000290760": 801)]
    ```




## Benchmark

There are a handful amount of open-sourced tools/software/scripts to calculate non-overlapping exon lengths, namely: Kooi [1], Sun [2], and Slowikowski [3, 4] scripts, and gtftools (-l flag) [5]. The Non-Overlapping Exon Length calculator (NOEL; referred just as "noel"), is introduced as a novel tool that outperforms the aforementioned software due to its remarkable performance. 

To assess the efficiency of noel and test the capabilities of other available scripts/tools, I used run times and memory usage estimates, based on 5 consecutive runs. This evaluation focused on two major gene annotation formats: GTF and GFF. It is worth nothing, however, that only 3 tools are capable of handling GFF files: Slowikowski, Sun* (described below) and noel. Before any batch of runs, I first modified each script to be CLI-responsive. Additionally, I further edited Sun's script to be able to handle GFF inputs by changing a regex pattern. No performance enhance-related changes or breaking structural modifications were applied.

Lastly, to evaluate the output consistency of the top-ranked tools (Sun, gtftools and noel), three species were used: *Homo sapiens* (GRCh38, GENCODE 44), *Canis lupus familiaris* (ROS_Cfam_1.0, Ensembl 110), and *Mus musculus* (GRCm39, GENCODE M33). 


    


The diverse methodologies to calculate non-overlapping exon lengths led to noticeable differences in run times. While Kooi and Slowikowski scripts were the last ranked (>250s for GENCODE 44) with GTF files and Slowikowski only for GFF files (~300s for GENCODE 44); Sun, gtftools and noel were the most efficient options (<50s for GENCODE 44). When analyzing these top-ranked tools, it is quickly perceived the noel's dominance over its competitors. For GTF files, noel achieves noticeably faster computation times when compared to gtftools (x4.3 faster; 4.2s vs 17.9s) and to Sun's script (x10.9 speedup; 4.2s vs 45.7s). On the other hand, noel performs the calculations on GFF3 x12.6 times faster than Sun's script (3.9s vs 49.7s).


    


A similar pattern is seen when examining memory usage estimates based on GTF files. Three distinct groups of tools can be identified: high-memory-consuming tools (Sun, Slowikowski, and Kooi), tools with moderate memory usage (gtftools), and the most memory-efficient option (noel). Here, noel exhibited a significantly lower memory usage when compared to gtftools (x9.1 less; 42.9 Mb vs 391.8 Mb) and to Kooi (x73.1 less; 42.9 Mb vs 3.1 Gb). With GFF files, on the other hand, noel achieved a striking x146.1-fold reduction in memory usage compared to Slowikowski (62,700 genes).  



    


The comparison of output from the top-ranked tools, including Sun, gtftools, and noel, yielded consistently paired estimates for each species, resulting in a high correlation (R = 0.99). Notably, both noel and Sun's script demonstrated a one-to-one correspondence for every gene in all tested annotation models. In contrast, gtftools exhibited limitations in processing genes, with a slight deficiency in the human and mouse models (0.05% and 0.06%, respectively), and a more substantial shortfall in the dog model (26%). Furthermore, noel outperformed the other tools, significantly improving runtime efficiency in both the mouse and dog models, with a speedup of at least 2.3 times.

Based on this comparative analysis between existing scripts/software to calculate non-overlapping exonic lengths and noel, it is evident that this tool represents a significant improvement. These findings unveil the potential of noel as a valuable resource to provide a fast and efficient way to automate non-overlapping exon length calculations.

## References

[1] https://www.biostars.org/p/83901/

[2] https://gist.github.com/jsun/aeca04ee2c5b5cc53ad795b660edd6c3

[3] https://gist.github.com/slowkow/8101481

[4] https://gist.github.com/slowkow/8101509#file-coding_lengths-py

[5] Hong-Dong Li, Cui-Xiang Lin, Jiantao Zheng, GTFtools: a software package for analyzing various features of gene models, Bioinformatics, Volume 38, Issue 20, 15 October 2022, Pages 48064808, https://doi.org/10.1093/bioinformatics/btac561

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