Question: Problem using SED for change IDs in gff file
0
gravatar for luciabilbao03
10 months ago by
luciabilbao030 wrote:

Hi,

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?

Thanks!

sed gff • 243 views
ADD COMMENTlink modified 10 months ago by _r_am32k • written 10 months ago by luciabilbao030

what is the output of

cat -n bovis_PROKKA.gff | sed 's/ILINNGPN_01481/tfpI/g' | grep -n tfpI
ADD REPLYlink written 10 months ago by Pierre Lindenbaum133k

Thanks Pierre for that line!

ADD REPLYlink written 10 months ago by luciabilbao030
1
gravatar for rbagnall
10 months ago by
rbagnall1.7k
Australia
rbagnall1.7k wrote:

Sed command has ILINNGPN_01481

You are looking at ILINNGPN_01482 in the before file

ADD COMMENTlink modified 10 months ago • written 10 months ago by rbagnall1.7k

Thanks rbagnall! rigth then I posted this I realize that! That's what was happening

ADD REPLYlink written 10 months ago by luciabilbao030
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