ATG

ATG is a library to handle and convert different data formats used in Genomics and Transcriptomics. The library provides convenient APIs to parse GTF and RefGene data and work with the resulting transcripts for all kind of downstream analyses.

The binary can be used to convert GTF into RefGene data and vice versa.

The main purpose is actually just that - convert a GTF file into a RefGene file. Surprsingly, there are not many tools to do this properly. Even atg does not handle all edge cases of GTF - but I tried to handle as much as possible. In addition, transcripts can also be written in bed format as well.

The project started only because I wanted to learn Rust. You will see that some sections have really bad code, others will have some better and more improved code. Overall, I'm still very new to Rust and I'm sure I fell for many traps and use lots of unidiomatic code. I'm happy for any feedback and improvement suggestions.

The library is still in its infancy but works so far and can handle what it's supposed to do. The current API is probably going to change a lot in future updates, so be careful of using atg in production or other critical workflows.

Usage

ATG command line tool

Install

The easiest way to install ATG is to use cargo (if you have cargo and rust installed)

cargo install atg

Run

Convert a GTF file to a RefGene file

atg --from gtf --to refgene --input /path/to/input.gtf --output /path/to/output.refgene

Convert RefGene to GTF

atg --from refgene --to gtf --input /path/to/input.refgene --output /path/to/output.gtf

Convert RefGene to bed

atg --from refgene --to bed --input /path/to/input.refgene --output /path/to/output.bed

Yes, that's it. Nothing more at the moment.

Ok, you can also change the verbosity, by adding -v (show info messages), -vv (debug), -vvv (trace)

On most Linux systems, you can use --input /dev/stdin and/or --output /dev/stdout to pipe into and out of atg.

Of course, all commands also have shorthand parameters:

• -f, --from
• -t, --to
• -i, --input
• -o, --output

ATG as library

The library API is mostly documented inline and available on docs.rs

Examples

Convert GTF to RefGene

use atg::gtf::Reader;
use atg::refgene::Writer;
use atg::models::{TranscriptRead, TranscriptWrite};

let mut reader = Reader::from_file("path/to/input.gtf")
    .unwrap_or_else(|_| panic!("Error opening input file."));

let mut writer = Writer::from_file("path/to/output.refgene")
    .unwrap_or_else(|_| panic!("Unable to open output file"));

let transcripts = reader.transcripts()
    .unwrap_or_else(|err| panic!("Error parsing GTF: {}", err));

match writer.write_transcripts(&transcripts) {
    Ok(_) => println!("Success"),
    Err(err) => panic!("Error writing RefGene file: {}", err)
};

ToDo / Next tasks

• Add to crates.io
• Bed module to generate bed files with exons and introns
• Compare transcripts from two different inputs
• Add fasta reading from BioRust for nt and aa sequence outputs

Known issues

GTF parsing

• NM_001371720.1 has two book-ended exons (155160639-155161619 || 155161620-155162101). During input parsing, book-ended features are merged into one exon