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NCBI Prokaryotic Genome Annotation Pipeline
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[FEATURE REQUEST] <Turn Off GO annotation> #280

Closed greg-harhay closed 5 months ago

greg-harhay commented 7 months ago

Could you provide an option/switch to turn off GO annotation? Such a switch is not described in the output of

pgap.py --help

Thank you.

Greg

azat-badretdin commented 7 months ago

Thank you for you report, Gregory!

Currently we do not provide an option to turn off the GO annotation.

I suppose an adventorous user could try a hacky way to do that by editing away GO lines in our SQLITE3 database of PFM attributes...

greg-harhay commented 7 months ago

Hi Azat, thanks for the quick reply. Bing and Bard searches for turning off the GO annotation in PGAP suggest that this option was available in the past, but then again, those might be AI hallucinations.

azat-badretdin commented 7 months ago

Bing and Bard searches for turning off the GO annotation in PGAP suggest that this option was available in the past

Thanks for letting us know, Gregory!

thibaudnis commented 7 months ago

Can you explain why you would be interested in turning off GO annotation? This is the first time we receive this request. Thanks!

greg-harhay commented 7 months ago

Sure, I want to add my own GO annotations and EC numbers and compare to the NCBI annotated genomes.

thibaudnis commented 7 months ago

We are not planning to add a switch for GO and EC in PGAP unless we perceive there is a wide need for this feature. May I ask what alternative method you plan on using?

greg-harhay commented 7 months ago

I am developing a custom approach. If it offers advantages to existing annotation, I'll publish it.