oggmap gtf2t2g -h
usage: oggmap <sub-command> gtf2t2g [-h] [-i I] [-o O] [-g] [-b] [-p] [-v] [-s] [-q] [-overwrite OVERWRITE]
options:
-h, --help show this help message and exit
-i I specify GTF input file
-o O specify output file [optional]
-g specify if gene names should be appended if they exist
-b specify if gene biotype should be appended if they exist
-p specify if protein id should be appended if they exist
-v specify if gene/transcript/protein version should be appended
-s specify if summary should be printed
-q specify if output should be quite
-overwrite OVERWRITE specify if existing output file should be overwritten (default: True)
gtf2t2g example:
# to get GTF from Mus musculus on Linux run:
$ wget https://ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.chr.gtf.gz
# on Mac:
$ curl https://ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.chr.gtf.gz --remote-name
# create t2g from GTF:
$ gtf2t2g -i Mus_musculus.GRCm39.108.chr.gtf.gz -o Mus_musculus.GRCm39.108.chr.gtf.t2g.tsv -g -b -p -v -s