A high-performance 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 bed2gtf gene 17266470 17285418 . + . gene_id "ENSG00000151743";
chr27 bed2gtf transcript 17266470 17281218 . + . gene_id "ENSG00000151743"; transcript_id "ENST00000541931.8";
chr27 bed2gtf exon 17266470 17266572 . + . gene_id "ENSG00000151743"; transcript_id "ENST00000541931.8"; exon_number "1"; exon_id "ENST00000541931.8.1";
...
in a few seconds.
Converts
- Homo sapiens GRCh38 GENCODE 44 (252,835 transcripts) in 3.25 seconds.
- Mus musculus GRCm39 GENCODE 44 (149,547 transcritps) in 1.99 seconds.
- Canis lupus familiaris ROS_Cfam_1.0 Ensembl 110 (55,335 transcripts) in 1.20 seconds.
- Gallus galus bGalGal1 Ensembl 110 (72,689 transcripts) in 1.36 seconds.
What's new on v.1.9.2
- Adds
--no-geneflag to only perform conversion without isoforms!- Modifies
-ito be required unless--no-genemode is present.- Refactors BedRecord.
- Isolates CLI as owned mod.
Usage: bed2gtf[EXE] --bed/-b <BED> --isoforms/-i <ISOFORMS> --output/-o <OUTPUT>
Arguments:
-b, --bed <BED>: a .bed file
-i, --isoforms <ISOFORMS>: a tab-delimited file
-o, --output <OUTPUT>: path to output file
-g, --gz[=<FLAG>] Compress output file [default: false] [possible values: true, false]
-n, --no-gene[=<FLAG>] Flag to disable gene_id feature [default: false] [possible values: true, false]
Options:
--help: print help
--version: print version
--threads/-t: number of threads (default: max ncpus)
--gz: compress output .gtfWarning
All the transcripts in .bed file should appear in the isoforms file.
click for detailed formats
bed2gtf just needs two files:
-
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 ENST00000595977you can build a custom file for your preferred species using Ensembl BioMart.
to install bed2gtf on your system follow this steps:
- get rust:
curl https://sh.rustup.rs -sSf | shon unix, or go here for other options - run
cargo install bed2gtf(make sure~/.cargo/binis in your$PATHbefore running it) - use
bed2gtfwith the required arguments - enjoy!
to build bed2gtf from this repo, do:
- get rust (as described above)
- run
git clone https://github.com/alejandrogzi/bed2gtf.git && cd bed2gtf - run
cargo run --release -- -b <BED> -i <ISOFORMS> -o <OUTPUT>
to build the development container image:
- run
git clone https://github.com/alejandrogzi/bed2gtf.git && cd bed2gtf - initialize docker with
start dockerorsystemctl start docker - build the image
docker image build --tag bed2gtf . - run
docker run --rm -v "[dir_where_your_gtf_is]:/dir" bed2gtf -b /dir/<BED> -i /dir/<ISOFORMS> -o /dir/<OUTPUT>
to use bed2gtf through Conda just:
conda install bed2gtf -c biocondaorconda create -n bed2gtf -c bioconda gtfsort
bed2gtf will send the output directly to the same .bed file path if you specify so
bed2gtf annotation.bed isoforms.txt output.gtf
.
├── ...
├── isoforms.txt
├── annotation.bed
└── output.gtf
where output.gtf is the result.
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 gene_id attributes (duplicated transcript_ids) if no refTable is included b) append 3rd column gene features.
This is an example:
chr27 stdin transcript 17266470 17281218 . + . gene_id "ENST00000541931.8"; transcript_id "ENST00000541931.8";
chr27 stdin exon 17266470 17266572 . + . gene_id "ENST00000541931.8"; transcript_id "ENST00000541931.8"; exon_number "1"; exon_id "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 . + . peak_id "chr20_50222035_50222038";
chr20 ---- peak 50188548 50189130 . + . peak_id "chr20_50188548_50189130";
and others (4) just provide exon-related information:
chr20 ensembl exon 50222035 50222038 . + . gene_id "ENST00000595977.1735"; transcript_id "ENST00000595977.1735"; exon_number "0
chr20 ensembl exon 50188548 50188930 . + . gene_id "ENST00000595977.3403"; transcript_id "ENST00000595977.3403"; exon_number "0
This is where bed2gtf comes in: a fast and memory efficient BED-to-GTF converter written in Rust. In ~4 seconds this tool produces a fully functional GTF converted file with all the needed features needed for post-processing tools.
bed2gtf is basically the reimplementation of C binaries merged in 1 step. This tool evaluates the position of k exons in j transcript, calculates start/stop/codon/UTR positions preserving reading frames and adjust the index + 1 (to be compatible with GTF convention). The isoforms file works as the refTable in C binaries to map each transcript to their respective gene; however, bed2gtf takes advantage of this and adds an additional "gene" line (to be compatible with other tools).
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