Entering edit mode
3.2 years ago
luciabilbao03 • 0
I want to use SED to change the names ID in a GFF file. I just want to change "ILINNGPN_01481" that appears only once for "tfpI" in the whole file. I am using the simplest line:
sed 's/ILINNGPN_01481/tfpI/g' bovis_PROKKA.gff > bovis_PROKKA_edited.gff
The IDs changes happened well, but suddenly the CDS coords also change for no reason.
looking for ILINNGPN_01482 in the file (Before):
NODE_16_length_55139_cov_21.7549 Prodigal:2.6 CDS 25370 26155 . - 0 ID=ILINNGPN_01482;inference=ab initio prediction:Prodigal:2.6;locus_tag=ILINNGPN_01482;product=hypothetical protein
looking for tfpI in the edited file (After):
NODE_16_length_55139_cov_21.7549 Prodigal:2.6 CDS 24581 25048 . + 0 ID=tfpI;inference=ab initio prediction:Prodigal:2.6,similar to AA sequence:GCF_002014975.1_ASM201497v1_genomic.gbff:WP_078275419.1;locus_tag=tfpI;product=pilin
Have a clue for what's going on here?
what is the output of
Thanks Pierre for that line!