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.
The easiest way to install ATG is to use cargo (if you have cargo and rust installed)
bash
cargo install atg
Convert a GTF file to a RefGene file
bash
atg --from gtf --to refgene --input /path/to/input.gtf --output /path/to/output.refgene
Convert RefGene to GTF
bash
atg --from refgene --to gtf --input /path/to/input.refgene --output /path/to/output.gtf
Convert RefGene to bed
bash
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
The library API is mostly documented inline and available on docs.rs
```no_run use atg::gtf::Reader; use atg::refgene::Writer; use atg::models::{TranscriptRead, TranscriptWrite};
let mut reader = Reader::fromfile("path/to/input.gtf") .unwraporelse(|| panic!("Error opening input file."));
let mut writer = Writer::fromfile("path/to/output.refgene") .unwraporelse(|| panic!("Unable to open output file"));
let transcripts = reader.transcripts() .unwraporelse(|err| panic!("Error parsing GTF: {}", err));
match writer.writetranscripts(&transcripts) { Ok() => println!("Success"), Err(err) => panic!("Error writing RefGene file: {}", err) }; ```