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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.

What's new on v.0.1.1

bed2gtff now can accept *.bed.gz and *.bed.zlib as inputs (~2s cost)

new dependencies have been added to support changes mentioned above

lib.rs can handle inserted blank spaces at the end of compressed files (bug)

the date watermark bug at the beginning of the files is now resolved!

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

Warning

All the transcripts in .bed file should appear in the isoforms file.

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

a .bed file

tab-delimited files with 3 required and 9 optional fields:

chrom   chromStart  chromEnd      name    ...
  |         |           |           |
chr20   50222035    50222038    ENST00000595977    ...

see BED format for more information

a tab-delimited .txt/.tsv/.csv/... file with genes/isoforms (all the transcripts in .bed file should appear in the isoforms file):
```
> cat isoforms.txt

ENSG00000198888 ENST00000361390
ENSG00000198763 ENST00000361453
ENSG00000198804 ENST00000361624
ENSG00000188868 ENST00000595977
```
you can build a custom file for your preferred species using Ensembl BioMart.

Installation

to install bed2gff on your system follow this steps:

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

Library

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

include bed2gff = 0.1.1 under [dependencies] in the Cargo.toml file
the library name is bed2gff, to use it just write:
```
use bed2gff::bed2gff; 
```
or
```
use bed2gff::*;
```

invoke

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

Build

to build bed2gff from this repo, do:

get rust (as described above)
run git clone https://github.com/alejandrogzi/bed2gff.git && cd bed2gff
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, .zlib)
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 (?)

bed2gff 0.1.1