GFF?

[lskatz]

Does anyone have a nice one liner to get GFF out of abricate output?

[lskatz]

n/m I guess BED will do it for me

cut -f 2-4 *.abricate.tsv | tail -n +2 > abricate.bed

[com31]

lskatz
Thank you for asking the question and providing the partial solution (excuse me as I could not write a proper gff3 after your steps). Could you please elaborate if you found a solution to this?
Any solution https://github.com/tseemann (even if multi-step solution)?

[lskatz]

My solution gives a bed file, and then if that is not sufficient, you can convert to a GFF from there. People have some partial solutions for that but I guess there isn't an exact conversion to GFF from BED.

For example:
https://bioinformatics.stackexchange.com/questions/2242/how-to-convert-bed-to-gff3

[com31]

Thank you lskatz for your help.
A discussion and developing solution is here
[https://bioinformatics.stackexchange.com/questions/20749/convert-abricate-output-tsv-file-to-gff3-format]
Could you too please help?