Closed ucassee closed 3 years ago
Hi,
yes, within the sqlite database provided with eggnog-mapper.
Best, Carlos
Hi @Cantalapiedra ,
Thanks for your reply. Where can I find the SQLite database? I wonder is it possible for me to get this database in csv or txt format?
Thanks
Hi @ucassee ,
the sqlite database is downloaded with download_eggnog_data.py
available in this repo.
You would need to extract the data. Something like:
sqlite3 data/eggnog.db "select * from prots limit 2" | tr "|" "\t"
You may also check the files in the downloads section of the eggNOG database web http://eggnog5.embl.de/#/app/downloads
I hope this helps.
Best, Carlos
Hi @Cantalapiedra ,
It helps a lot. I extracted the table I want, but it lost the column that contains detailed annotation (same as the last column in the following result of eggmapper).
Dive121-T1_NODE_78_20 1216007.AOPM01000080_gene1215 1.4e-35 156.0 Pseudoalteromonadaceae radC GO:0006139,GO:0006259,GO:0006281,GO:0006725,GO:0006807,GO:0006950,GO:0006974,GO:0008150,GO:0008152,GO:0009987,GO:0033554,GO:0034641,GO:0043170,GO:0044237,GO:0044238,GO:0044260,GO:0046483,GO:0050896,GO:0051716,GO:0071704,GO:0090304,GO:1901360 ko:K03630 ko00000 Bacteria 1MXZ5@1224,1RP86@1236,2Q0N1@267888,COG2003@1,COG2003@2 NA|NA|NA E Belongs to the UPF0758 family
Dive121-T1_NODE_78_21 1396141.BATP01000029_gene2258 1.6e-18 100.1 Verrucomicrobiae Bacteria 2E0FE@1,2IVPU@203494,32W1M@2,46TEN@74201 NA|NA|NA S Domain of unknown function (DUF932)
Thanks, Yingli
Hi @ucassee ,
the description returned by emapper is not from proteins but from the Orthologous Groups. It is using the "og" table, querying for "og.og" and "og.level".
Best, Carlos
Closing this. Please, reopen or reissue if needed.
Hi, Is there a table for annotation that links protein id in eggNOG_v5.proteomes.faa to the detail description? Thanks