Add additional groupings to optional stratified allele frequencies #523
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
jkgoodrich
approved these changes
Apr 5, 2023
gnomad/utils/annotations.py
Outdated
Comment on lines
425
to
426
| if additional_strata_grouping_expr is None: | ||
| additional_strata_grouping_expr = {} |
There was a problem hiding this comment.
could move up to if statement above so make above:
if additional_strata_grouping_expr is None:
additional_strata_grouping_expr = {}
else:
_freq_meta_expr = _freq_meta_expr.annotate(**additional_strata_grouping_expr)
gnomad/utils/annotations.py
Outdated
Comment on lines
530
to
534
| if strata not in cut_data.keys(): | ||
| raise KeyError( | ||
| "%s is not an existing annotation and thus cannot be combined with" | ||
| " additional strata" | ||
| ) |
There was a problem hiding this comment.
Will this ever happen? strata should be in cut_data right because it's added to _freq_meta_expr which is annotated as mt._freq_meta and that is used to build the cut_dict for the cut_data aggregation
There was a problem hiding this comment.
You're right it should not! This is an artifact of a previous approach, before we added additional_strata_groupings_expr to _freq_meta_expr- will remove this check.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Add additional groupings to optional stratified allele frequencies to allow stratified frequencies by multiple annotations: e.g. platform and population, or GATK version and population.