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opencobra / memote

memote – the genome-scale metabolic model test suite
https://memote.readthedocs.io/
Apache License 2.0
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Proper syntax for gene annotation ccds #686

Closed mjenior closed 4 years ago

mjenior commented 4 years ago

Problem description

Hi,

I'm trying to integrate consensus sequence annotations for genes in my model. I follow what seems to be the correct method like the other categories are listed in the report, Ex:

model.genes[3]annotation['ccds'] = 'ATCG'

But 0.0% are ever detected in the MEMOTE output. Is there a different way that this data should be added? Thanks!

Midnighter commented 4 years ago

At the moment, memote only checks the preconfigured list of annotation namespaces that you see in the report. This could be changed, although including the consensus sequences is not all too common, I suspect. (Except for ME-models.)

In the meantime you can create a custom test that works like the existing annotation tests.

mjenior commented 4 years ago

Got it. Thank you!

Midnighter commented 4 years ago

Closing this for now. If there are more requests for this, I'm happy to reopen the issue.