Tavi Nathanson
Tavi Nathanson
From @iskandr re https://github.com/hammerlab/mhctools/pull/86: > Followup to mhctools PR, a much smaller change to make Topiary work: https://github.com/hammerlab/topiary/pull/66 > The only API changes that should matter to you are `epitope_lengths`...
@jburos wrote some useful utilities in https://github.com/hammerlab/rcc-analyses/blob/master/analyses/epidisco.py and https://github.com/hammerlab/ovarian-msk-chemo/blob/master/epidisco/epidisco.py (the latter contains some additional utilities, I believe) that we should factor out into public code. One idea is a `discohorts`...
Per https://github.com/hammerlab/cohorts/pull/179#issuecomment-273334798
Per https://github.com/hammerlab/cohorts/pull/177#discussion_r96321375
Will require a test BAM.
From @tavinathanson: > I'm fairly unclear right now about how best, when using cohorts, to use epidisco results; for example using epidisco neoepitopes rather than https://github.com/hammerlab/cohorts/blob/master/cohorts/cohort.py#L767 > > One obstacle...
Currently, regular neoantigens use `topiary` while expressed neoantigens use `isovar` + `mhctools` because `topiary` doesn't use isovar. This depends on `topiary` making use of `isovar`, I think. Related: https://github.com/hammerlab/vaxrank/issues/31
We're currently frozen on `varcode` and `isovar`, and also have version limits on `topiary` and `mhctools`. We need to fix `cohorts` to work on the latest versions of all these...
Once that's done, `Patient` no longer needs to point to `Cohort`.
Seems very easy to accidentally forget the following lines at the beginning of functions: ``` filter_fn = first_not_none_param([filter_fn, cohort.filter_fn], no_filter) normalized_per_mb = first_not_none_param([normalized_per_mb, cohort.normalized_per_mb], False) ``` ...and thereby not use...