update compatibility to COG2014?

[sirmicrobe]

Hi Andreas,

Love the cdd2cog.pl script and description, thanks for making this available. Was wondering if you planned to update this to the newer release of COG ftp://ftp.ncbi.nlm.nih.gov/pub/COG/COG2014/data/ with the fun and whog updated to fun2003-2014.tab and cognames2003-2014.tab. I tried running cdd2cog.pl with these newer classification files and it doesn't seem to parse the COG categories and so the func_stats.txt file does not get populated.

[aleimba]

Hi @sirmicrobe,

I'm glad cdd2cog.pl is useful to you!

Well, ahem, planned to do this quite some time ago, never got around to do it. It's quite low priority on my ToDo list ... Frankly, I had this discussion with @tseemann over at his Prokka repo a while ago (tseemann/prokka#85). The COG update didn't include any more models but updated the assignment of existing COGs to new bacterial CDS (http://www.ncbi.nlm.nih.gov/pubmed/25428365). Thus, the main advantage you will have is a higher coverage of COGs for bacteria newly included (and an update of the annotation of previous hypothetical COGs).

If you can't wait I suggest you head over to JGI's IMG/ER annotation system and upload your genome(s) there. I'm guessing they updated to the new system (but haven't checked).

HTH,
Andreas

[embatty]

Really useful script so I've had a go at updating this to parse fun2003-2014.tab and cognames2003-2014.tab, and sent a pull request with the new version.