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Question: Prokka Python Script for Gene Annotation
0
gravatar for Fid_o
13 months ago by
Fid_o • 20
Fid_o • 20 wrote:

I have over 900 assembled genomes which I want to annotate using prokka. Previously I have annotated few sequences by running each one by one, but with 900 I need a python script to automate the process.

Can anyone share a script that can be adopted to do my annotation, please.

Regards.

linux prokka script annotation python • 497 views
ADD COMMENT • link •
modified 13 months ago by Mensur Dlakic • 8.2k • written 13 months ago by Fid_o • 20

Why do you think you need python? Since this is a straight command line you should be able to do this via a shell script.

ADD REPLY • link written 13 months ago by GenoMax ♦ 95k
1
gravatar for Mensur Dlakic
13 months ago by
Mensur Dlakic • 8.2k
USA
Mensur Dlakic • 8.2k wrote:

I second genomax suggestion to do this in shell scripts. Assuming your files have .fna extension and that you have bash shell:

for i in *.fna
do
prokka --outdir ${i%.fna} --force --prefix ${i%.fna} --locustag ${i%.fna} --rfam --cpus # $i
done

If you have C-shell:

foreach i ( *.fna )
prokka --outdir $i:r --force --prefix $i:r --locustag $i:r --rfam --cpus # $i
end

If all of them are the same genus and/or kingdom, you could add --genus and --kingdom switches as well. You may want to remove --rfam if not interested in non-coding RNAs because that part of the search is slowest. Also, specify a number instead of # after the --cpus switch.
ADD COMMENT • link modified 13 months ago • written 13 months ago by Mensur Dlakic • 8.2k
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