cohorts
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hammerlab
Utilities for analyzing mutations and neoepitopes in patient cohorts
Would be useful to have a doc explaining to users how to write their own filter functions.
In some cohorts we end up fitting long-running Stan models as part of the analysis process. It would be convenient to be able to cache these fitted objects (in much...
Here I'm trying to achieve a goal of allowing an analysis on a cohort where some but not all records have RNA sequencing data. Currently, if one is using a...
Added a variety of debug messages, also modified isovar cache so that the cached file varies according to the input variants provided. In the absence of this, I was seeing...
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,...
We use the caching functions a lot, but don't expose any simple primitives to make caching cleaner and less repetitive.
