bed2gff

A Rust BED-to-GFF3 translator.

translates

chr7 56766360 56805692 ENST00000581852.25 1000 + 56766360 56805692 0,0,200 3 3,135,81, 0,496,39251,

into

chr7 bed2gff gene 56399404 56805692 . + . ID=ENSG00000166960;gene_id=ENSG00000166960

chr7 bed2gff transcript 56766361 56805692 . + . ID=ENST00000581852.25;Parent=ENSG00000166960;gene_id=ENSG00000166960;transcript_id=ENST00000581852.25

chr7 bed2gff exon 56766361 56766363 . + . ID=exon:ENST00000581852.25.1;Parent=ENST00000581852.25;gene_id=ENSG00000166960;transcript_id=ENST00000581852.25,exon_number=1

chr7 bed2gff CDS 56766361 56766363 . + 0 ID=CDS:ENST00000581852.25.1;Parent=ENST00000581852.25;gene_id=ENSG00000166960;transcript_id=ENST00000581852.25,exon_number=1

...

chr7 bed2gff start_codon 56766361 56766363 . + 0 ID=start_codon:ENST00000581852.25.1;Parent=ENST00000581852.25;gene_id=ENSG00000166960;transcript_id=ENST00000581852.25,exon_number=1

chr7 bed2gff stop_codon 56805690 56805692 . + 0 ID=stop_codon:ENST00000581852.25.3;Parent=ENST00000581852.25;gene_id=ENSG00000166960;transcript_id=ENST00000581852.25,exon_number=3

...

in a few seconds.

Usage

Usage: bed2gff[EXE] --bed <BED> --isoforms <ISOFORMS> --output <OUTPUT>

Arguments:
    --bed <BED>: a .bed file
    --isoforms <ISOFORMS>: a tab-delimited file
    --output <OUTPUT>: path to output file

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

crate: https://crates.io/crates/bed2gff

Installation

to install bed2gff on your system follow this steps:

1. get rust: curl https://sh.rustup.rs -sSf | sh on unix, or go here for other options
2. run cargo install bed2gff (make sure ~/.cargo/bin is in your $PATH before running it)
3. use bed2gff with the required arguments
4. enjoy!

Library

to include bed2gff as a library and use it within your project follow these steps:

1. include bed2gff = 0.1.0 under [dependencies] in the Cargo.toml file

2. the library name is bed2gff, to use it just write:

   use bed2gff::bed2gff; 

   or

   use bed2gff::*;

3. invoke

   let gff = bed2gff(bed: &String, isoforms: &String, output: &String)

Build

to build bed2gff from this repo, do:

1. get rust (as described above)
2. run git clone https://github.com/alejandrogzi/bed2gff.git && cd bed2gff
3. run cargo run --release <BED> <ISOFORMS> <OUTPUT>(arguments are positional, so you do not need to specify --bed/--isoforms)

Output

bed2gff will send the output directly to the same .bed file path if you specify so

bed2gff annotation.bed isoforms.txt output.gff

.
├── ...
├── isoforms.txt
├── annotation.bed
└── output.gff3

where output.gff3 is the result.

FAQ

Why?

Converting formats is a daily practice in bioinformatics. This is way more common while working with gene annotations as tools differ in input/output layouts. GTF/GFF/BED are the most used structures to store gene-related annotations and the conversion needs are not well covered by available software.

A considerable portion of genomic tools reduce the software space by accepting GTF/GFF3 files only, directing BED users to translate their files into different formats. While some of this issues have already been covered (e.g. bed2gtf) with GTF files, the GFF3 layout lacks stable converting tools (1, 2).

bed2gff is presented as a straightforward option to convert BED files into ready-to-use GFF3 files, closing that gap.

How?

bed2gff, takes the base code of bed2gtf, that basically is the reimplementation of UCSC's C binaries merged in 1 step (bedToGenePred + genePredToGtf). Before any conversion, this tool sorts the .bed file internally using a similar algorithmic approach seen in gtfsort. This step allows bed2gff to directly present the output file sorted in a natural and convenient way. Then, evaluates the position of exons and other features (CDS, stop/start, UTRs), preserving reading frames and adjusting the indexing count.

Following the rationale of bed2gtf, bed2gff is able to produce a ready-to-use gff3 file by using an isoforms file, that works as the refTable in C binaries to map each transcript to their respective gene.

To Do's

• Allow users to input compressed files (e.g. .gz, .bgzip)
• Test GFF3 with different types of aligners
• Improve the error module
• Add test modules for most of the scripts
• Allow users to specify their parent/child relationships (?)

References

1. https://bioinformatics.stackexchange.com/questions/2242/how-to-convert-bed-to-gff3
2. https://www.biostars.org/p/2/