Open Zazgah opened 4 years ago
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 notifications@github.com 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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Thanks. I will go with this strategy as well.
Regards, Vincent
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!
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,