Can't simulate constant SHM with derived parameters

scharch commented 6 years ago

Seems like there should be a way to override SHM, while still keeping the derived recombination parameters (or vice versa).

partis simulate --parameter-dir ../v15/partis/mu/ --outfname partis_simulate.csv --n-sim-events 10 --n-leaves 1 --constant-number-of-leaves --mutate-from-scratch --same-mute-freq-for-all-seqs --flat-mute-freq 0 --only-genes IGHV1-69*10:IGHD3-10*01:IGHJ6*02
Traceback (most recent call last):
  File "/home/schrammca/bin/partis", line 423, in <module>
    args.func(args)
  File "/home/schrammca/bin/partis", line 63, in run_simulation
    raise Exception('you can\'t specify --parameter-dir if you also set either of the scratch options or --generate-germline-set')
Exception: you can't specify --parameter-dir if you also set either of the scratch options or --generate-germline-set

psathyrella commented 6 years ago

Yes. This was the idea with having --rearrange-from-scratch and --mutate-from-scratch separate. I think I added that ^ exception because at some later date I changed some things about how the options worked, and I wanted to go back through and make sure that specifying them separately still worked as intended. OK, will go do that now...

psathyrella commented 6 years ago

OK I've separated --rearrange-from-scratch and --mutate-from-scratch, and hopefully clarified them and the related options. lmk if it doesn't behave as expected.

https://github.com/psathyrella/partis/commits/dev

psathyrella commented 6 years ago

switched interface a bit (to clarify what's coming from where) so using --shm-parameter-dir and --reco-parameter-dir instead of --parameter-dir when simulation from scratch.

https://github.com/psathyrella/partis/commit/b0c45c4e1ad884ab2b61ebc2dc52ba43dd60458f

psathyrella / partis

Can't simulate constant SHM with derived parameters #246