[FEATURE REQUEST] Adding a program to annotate viral PHROGs via their HMMs

[ivagljiva]

A small project to improve anvi'o, based upon feedback/ideas @FlorianTrigodet and I heard from our colleagues at the QIB in Norwich.

The need

The PHROGs database contains orthologous groups of proteins from viruses. You can download their HMMs, but currently annotating them in anvi'o contigs databases would require either 1) running HMMER yourself and importing the resulting functions, or 2) making a custom HMM source out of the PHROGs and running them with anvi-run-hmms.

The solution

We could implement a program similar to anvi-run-kegg-kofams or anvi-run-pfams for the PHROGs database.

Beneficiaries

Those who study viruses in anvi'o.

[Ge0rges]

I may try to take a stab at this after ISME. I've written scripts to make custom HMM sources so I have those already, and wanted to look at viral stuff in my metagenome anyway. If someone else wants to work on this maybe we can help each other out let me know!

[Ge0rges]

@ivagljiva would you rather see an implementation like what was done for the MDM Defense Finder HMMs with an anvi-script-gen-phrogs-hmm-directory command, or something more integrated such as anvi-run-phrogs? I guess the precedent I established for these was to make directories easily accessible but I guess there's a conversation be had here about what makes the most sense.

[meren]

Hi @Ge0rges, I just wanted to quickly come in and let you know that everyone is on vacation, and that's why we have been a bit quiet on Discord and GitHub. We will catch up with all these threads as people will start coming back in soon :)