Georges Kanaan

Hey @ArtRand, I was wondering if you had any data or recollection of how well positional DMR correlated to KS d-values? (i.e., the higher the d-value, the more DMRs I...

All good, thank you. I can conduct this on my own and report back if it is of interest.

Also I've noticed sometimes the output `regions.bed` is empty with no error printed?

Hey @ArtRand could you let me know what schema for the output is when `--regions` is specified?

Seems like the pulp dependency is really an issue of snakemake that's on the way to being solved. For now we might want to keep it included, and remove it...

@meren what do you think about defaulting to `pyrodigal-gv` as Florian suggested? Looking into it briefly It seems that the viral models are added, so I think this would be...

I think it's more user friendly to keep the flags named the same way. The underlying engine is still prodigal after all.

@FlorianTrigodet I believe the function you removed from utils is also used on [line 15 ](https://github.com/merenlab/anvio/blob/b45d10156ddafd60cdfa0a6f543219aa2495b99b/anvio/data/hmm/__init__.py#L15)in `anvio/data/hmm/__init__.py` . So importing `anvio.data.hmm` currently crashes (e.g. when running `anvi-run-hmms`). Only found this...

@FlorianTrigodet any chance this could be merged soon?

Hmm actually running with `--prodigal-single-mode` gives the following. Identical command without that parameter works. ``` Traceback for debugging ================================================================================ File "/Accounts/gkanaan/github/anvio/bin/anvi-gen-contigs-database", line 64, in main(args) File "/Accounts/gkanaan/github/anvio/anvio/terminal.py", line 926, in...