EnTAP v0.9.2-beta Incompatible with emapperdb-5.0.0

[selveyad]

Howdy,

I was wondering if there were any plans in the works (or in motion) to update the EggnogDatabase.cpp/h to incorporate the new database format of emapperdb-5.0.0?

The current database structure is similar to emapperdb-4.5.1, but is missing the GO_freq, KEGG_freq, SMART_freq, and proteins columns in the og table. I want to utilize EnTAP the whole way through, but also wanted to utilize the most updated information from EggNOG. If there aren't any plans to update EnTAP to incorporate emapperdb-5.0.0, I can just use v4.5.1 for EnTAP and then merge results from eggnog-mapper using v5.0.0.

Thanks!

Alex

[harta55]

Hi,

This is definitely on the radar to update the compatibility to the new database. However, right now the focus is support for Transdecoder, BUSCO, and integration with Galaxy so it may not be for at least another 6-8 weeks before this gets worked on!

-Alex

[selveyad]

Hey Alex,

Definitely, seems like there is a lot of integration happening which is exciting! I am trying to work the db to produce similar rows, but I don't think they will contain the same information. I'll probably run EnTAP with the 4.5.1 db while I try to jury-rig the 5.0.0 db to produce similar output like the *_freq columns. I'm not sure why they took those out, they contained the most useful information all packaged up in a single column! Anyway, good luck! keep us updated!

Best Regards,

Alex

[Cantalapiedra]

Hi,

I am not sure why they were removed, but I am almost sure that they were not being used at all in eggnog-mapper, at least since the addition of the logic to deal with different kinds of co-orthology.

Best, Carlos

[Aciole-David]

Hello there, Any update with emapper 5?