A fast bed-to-gtf converter written in Rust.
translates
chr27 17266469 17281218 ENST00000541931.8 1000 + 17266469 17281218 0,0,200 2 103,74, 0,14675,
into
```
chr27 stdin gene 17266470 17281218 . + . geneid "ENSG00000151743"; genebiotype "protein_coding";
chr27 stdin transcript 17266470 17281218 . + . geneid "ENSG00000151743"; transcriptid "ENST00000541931.8";
chr27 stdin exon 17266470 17266572 . + . geneid "ENSG00000151743"; transcriptid "ENST00000541931.8"; exonnumber "1"; exonid "ENST00000541931.8.1";
... ```
in a few seconds.
``` rust
Usage: bed2gtf[EXE] --bed
Arguments:
--bed
Options: --help: print help --version: print version ```
click for detailed formats
bed2gtf just needs two files: 1. a .bed file tab-delimited files with 3 required and 9 optional fields: ``` chrom chromStart chromEnd name ... | | | | chr20 50222035 50222038 ENST00000595977.1735 ... ``` see [BED format](https://genome.ucsc.edu/FAQ/FAQformat.html#format1) for more information 2. a tab-delimited .txt/.tsv/.csv/... file with genes/isoforms: ``` > cat isoforms.txt ENSG00000198888 ENST00000361390 ENSG00000198763 ENST00000361453 ENSG00000198804 ENST00000361624 ``` you can build a custom file for your preferred species using [Ensembl BioMart](https://www.ensembl.org/biomart/martview).
to install bed2gtf 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 bed2gtf (make sure ~/.cargo/bin is in your $PATH before running it)
4. use bed2gtf with the required arguments
5. enjoy!
to include bed2gtf as a library and use it within your project follow these steps:
1. include bed2gtf = 1.1.0 under [dependencies] in the Cargo.toml file
2. the library name is bed2gtf, to use it just write:
``` rust
use bed2gtf::bed2gtf;
```
or
``` rust
use bed2gtf::*;
```
3. invoke
rust
let gtf = bed2gtf(bed: PathBuf, isoforms: PathBuf)
to build bed2gtf from this repo, do:
git clone https://github.com/alejandrogzi/bed2gtf.git && cd bed2gtfcargo run --release <BED> <ISOFORMS>(arguments are positional, so you do not need to specify --bed/--isoforms)bed2gtf will send the output directly to the same .bed file path
.
├── ...
├── isoforms.txt
├── annotation.bed
└── output.gtf
where output.gtf is the result. Any intermediate files are deleted, since there is no need to keep them.
UCSC offers a fast way to convert BED into GTF files through KentUtils or specific binaries (1) + several other bioinformaticians have shared scripts trying to replicate a similar solution (2,3,4).
A GTF file is a 9-column tab-delimited file that holds gene annotation data for a specific assembly (5). The 9th column defines the attributes of each entry. This field is important, as some post-processing tools that handle GTF files need them to extract gene information (e.g. STAR, arriba, etc). An incomplete GTF attribute field would probably lead to annotation-related errors in these software.
Of the available tools/scripts mentioned above, none produce a fully functional attribute GTF file conversion. (1) uses a two-step approach (bedToGenePred | genePredToGtf) written in C, which is extremely fast. Since a .bed file does not preserve any gene-related information, this approach fails to a) include correct geneid attributes (duplicated transcriptids) b) append 3rd column gene features.
This is an example:
``` chr27 stdin transcript 17266470 17281218 . + . geneid "ENST00000541931.8"; transcriptid "ENST00000541931.8";
chr27 stdin exon 17266470 17266572 . + . geneid "ENST00000541931.8"; transcriptid "ENST00000541931.8"; exonnumber "1"; exonid "ENST00000541931.8.1"; ```
On the other hand, available scripts (2,3,4) fall into bad-formatted outputs unable to be used as input to other tools. Some of them show a very customed format, far from a complete GTF file (2):
``` chr20 ---- peak 50222035 50222038 . + . peakid "chr2050222035_50222038";
chr20 ---- peak 50188548 50189130 . + . peakid "chr2050188548_50189130"; ``` and others (4) just provide exon-related information:
``` chr20 ensembl exon 50222035 50222038 . + . geneid "ENST00000595977.1735"; transcriptid "ENST00000595977.1735"; exon_number "0
chr20 ensembl exon 50188548 50188930 . + . geneid "ENST00000595977.3403"; transcriptid "ENST00000595977.3403"; exon_number "0 ```
This is where bed2gtf comes in: a fast and memory efficient BED-to-GTF converter written in Rust. In ~15 seconds this tool produces a fully functional GTF converted file with all the needed features needed for post-processing tools.
bed2gtf takes advantage of UCSC binaries. These executables show slightly lower computation times than those seen in a similar rust implementation. This tool uses bedToGenePred + genePredToGtf as a first step, automates their download and updates permissions. After that, this tool overcomes the limitations of geneid and gene-feature fields by expecting a tab-delimited isoforms file. Each unique transcript seen in the new gtf file is mapped to their respective geneid. With this information, bed2gtf simply constructs gene-feature lines and corrects gene_ids.
At the time of bed2gtf being publicly available some gaps have not been covered yet.