Jacki Buros Novik
Jacki Buros Novik
A few changes ended up in this PR: * Refactored summary functions, so they are now composable. IE `only_nonsynonymous(snv_count)` returns a function equivalent to `nonsynonymous_snv_count`. Similarly, `only_exonic(only_nonsynonymous(snv_count))` returns the count...
As it stands, this function likely contains a lot of repeated logic & probably also has too many checks (for io errors, no variants, etc). See https://github.com/hammerlab/cohorts/pull/245#discussion_r134777391 for some context.
We added some new parameters in a recent PR - #245: 1. `fail_on_missing_bams` 2. `fail_on_missing_variants` 3. `fail_on_missing_hla` We should add some test cases for these.
The way our logging module is configured isn't quite right - I don't know what the best practice is (seems there are [multiple recommendations on SO](https://stackoverflow.com/questions/15727420/using-python-logging-in-multiple-modules)). At the very least,...
Often when caching results there are logger warnings, info messages and possible errors that are reported on cache generation but are lost once the result has been cached. The majority...
Encountered an error when using `expressed_neoantigen_count` in the course of an analysis: This did not occur for all patients, but did occur for approximately 3 patients. Here is a sample...
@tavinathanson brought up a good point, that we should allow a case of plotting survival `on=None`, by default. Which would plot survival for the cohort overall, not by a covariate...
Certain parts of readme & other documentation are out of date. 1. [ ] Notably, the README contains references to `snv_vcf_paths=`, which should now be `variants=`. 2. [ ] The...
We should let people know why predicted neoantigens are NaN for patients without HLA type data.
Getting the following error when trying to estimate `median_vaf_purity` on a combined/merged VCF file. ```python /home/jacquelineburos/projects/cohorts/cohorts/functions.py in grab_vaf(variant) 271 def grab_vaf(variant): 272 filterable_variant = FilterableVariant(variant, variants, patient) --> 273 return...