gxf2chrom

Everything in .chrom from GTF/GFF files.

turns GTF/GFF files into:

ENSP00000501388.1       chr1    -       19417068        19485438
ENSP00000438792.1       chr11   -       72754899        72781181
ENSP00000224756.8       chr10   +       84371052        84513540
ENSP00000415935.1       chr2    +       215312481       215349652

Some stast on different species:

• Homo sapiens GRCh38 GENCODE 44 (252,835 transcripts) in 1.84 seconds.
• Mus musculus GRCm39 GENCODE 44 (149,547 transcritps) in 1.02 seconds.
• Canis lupus familiaris ROS_Cfam_1.0 Ensembl 110 (55,335 transcripts) in 0.57 seconds.
• Gallus galus bGalGal1 Ensembl 110 (72,689 transcripts) in 0.62 seconds.

Usage

Usage: gxf2chrom [OPTIONS] --input <GXF> --output <CHROM>
 
Arguments:
    --input/-i <GXF>: a .gtf/gff/*.gz file
    --output/-o <CHROM>: path to output .chrom file

Options:
    --help/-h: print help
    --version/-v: print version
    --feature/-f: feature to extract [default: protein_id]
    --threads/-t: number of threads [default: max ncpus]

Installation

to install gxf2chrom 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 gxf2chrom (make sure ~/.cargo/bin is in your $PATH before running it)
3. use gxf2chrom with the required arguments
4. enjoy!

Build

to build gxf2chrom from this repo, do:

1. get rust (as described above)
2. run git clone https://github.com/alejandrogzi/gxf2chrom.git && cd gxf2chrom
3. run cargo run --release -- -i <GXF> -o <CHROM> [OPTIONS]

Container image

to build the development container image:

1. run git clone https://github.com/alejandrogzi/gxf2chrom.git && cd gxf2chrom
2. initialize docker with start docker or systemctl start docker
3. build the image docker image build --tag gxf2chrom .
4. run docker run --rm -v "[dir_where_your_gxf_is]:/dir" gxf2chrom -i /dir/<GXF> -o /dir/<CHROM>

Conda

to use gxf2chrom through Conda just:

1. conda install gxf2chrom -c bioconda or conda create -n gxf2chrom -c bioconda gtfsort

Benchmark

This tool was inspired by NCBIgff2chrom.py from the Oxford dot plots repository. to quickly convert GTF/GFF files into .chrom files. Here is a quick benchmark:

With faster times, gxf2chrom intends to be a versatile approach to be implemented in any pipeline!