Closed rzlim08 closed 3 years ago
One design note. I see that you are calling the utils like a binary from bash. What are your thoughts about calling them via python like?
python3 <<< CODE from idseq_utils import foo foo(~{some_thing}) CODE
I think this is a great idea! I didn't think of it, but it would probably be better than the current solution. I'll see if I can convert this.
@morsecodist
The python scripts should have been replaced by inline code here. I haven't replaced the read_descriptions util, as I think it may be better to rethink/rewrite our descriptions in general.
This might be a bit of a heavy PR. I pulled some of the functions out of idseq-dag and put them into idseq_utils in order to make them standalone functions. As this matures, we may will want to make this into a separate repository.
The current tests and benchmarks seem to pass, I'm still making new ones to cover the different cases.