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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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Problems of database related codes #55

Open 444thLiao opened 2 years ago

444thLiao commented 2 years ago

Dear author,

I found out that there are a huge amount of lines in your codes using the VOG ID directly. But when I use the latest/another version of VOG db. This might be a disaster since the VOG ID would be changed. I think it should reconstruct those codes in a more descent way. Best regards

KrisKieft commented 2 years ago

Hi,

This is a known downside to the way VIBRANT was initially coded. For now the intended VOG version functions well. There is no functionality to use an updated/different version.

444thLiao commented 2 years ago

Thanks!

I noticed that there are lots of defined IDs within the codes. I wonder that if I want to change the VOG version by myself, is there any codes I need to revise also except for the names list within the folder 'files'.

KrisKieft commented 2 years ago

It's more than just the VOG names. First, I can't guarantee the machine learning model will behave similarly with a new database as that hasn't been tested. Also, each VOG comes with a v-score and those would need to be updated as well.