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tseemann
Can prokka annotate only from --protein file?
Dear tseemann
I've been using prokka and it's an amazing tool. Thank you for your contribution to the scientific community.
I am wondering if I can use prokka from anotalty ONLY from the file provided by --proteins [X]
In my current scenario I only want to annotate my proteins of interest, not the ones provided in default database.s If I clear the default database, prokka still ask to generate it.
Thank you very much for your time,
Hi @Zazgah
Did you come up with any solution? I have a similar task to do as well.
Not yet.
I have just added a text tag to the proteins of interest (for example -ZazgahProteins-). And then after annotattion i've filtered all the features that containing such string.
Not the most elegant but it works!
Best,
On Fri, Oct 9, 2020 at 5:43 PM vincentappiah [email protected] wrote:
Hi @Zazgah https://github.com/Zazgah
Did you come up with any solution? I have a similar task to do as well.
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What does your .faa file look like? I don't know which format the header should be in for prokka to actually annotate the CDS accoridng to my .faa file.
@avonm did you figure this out? I can only get --proteins to work with an faa downloaded directly from NCBI but not one that I've curated myself.
@mikeyweigand I did get it to work but now I have switched to bakta. The header in the proteins file look like this:
ABV20485.1 2.7.2.4~~~thrA~~~aspartokinase/homoserine dehydrogenase I AY513487.1 ~~~cosD~~~PCFO71 CosD adhesin~~~
The last header line is from my own database and those headers were manually formated.
Hope this helps!