zgtf

gtf conversion utlity

Installation

# clone the repo
git clone https://github.com/zavolanlab/zgtf.git
# create a virtual environment
python3 -m venv venv
# activate the virtual environment
source venv/bin/activate
# install zgtf scripts
pip install .

Run

Convert gtf file to bed12

gtf2bed12 --gtf <INPUT.gtf> --bed12 <OUTPUT.bed> --verbose

arguments:
  -h, --help            show this help message and exit
  --gtf FILE            Annotation file (gtf format)
  --bed12 FILE          Output file (bed12 format)
  --transcript_type TRANSCRIPT_TYPE
                        Transcript type [Default: protein_coding]
  -v, --verbose         Verbose

Docker

Pull image

docker pull zavolab/zgtf

Run

docker run -it zavolab/zgtf gtf2bed12 --help

Singularity

Pull image

singularity pull docker://zavolab/zgtf

Run

singularity exec zgtf_latest.sif gtf2bed12 --help