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tseemann / abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
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GFF? #187

Open lskatz opened 2 years ago

lskatz commented 2 years ago

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

lskatz commented 2 years ago

n/m I guess BED will do it for me

cut -f 2-4 *.abricate.tsv | tail -n +2 > abricate.bed
com31 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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?