TopiaryPredictor #81
Merged
TopiaryPredictor #81
Conversation
This file contains 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
…having to pass very large number of arguments
julia326
reviewed
Dec 20, 2017
topiary/predictor.py
Outdated
| expressed above this threshold. | ||
|
|
||
| transcript_expression_threshold : float, optional | ||
| If transcript_expression_dict is given, only keep effects on |
There was a problem hiding this comment.
Is it possible to rephrase this docstring so that you don't need to search for what transcript_expression_dict is?
|
|
||
| padding_around_mutation : int | ||
| How many residues surrounding a mutation to consider including in a | ||
| candidate epitope. Default is the minimum size necessary for epitope |
There was a problem hiding this comment.
where is this default set? In the constructor you just keep the passed-in value
There was a problem hiding this comment.
Clarified the default by moving check_padding_around_mutation call to __init__.
topiary/predictor.py
Outdated
| ---------- | ||
| effects : Varcode.EffectCollection | ||
|
|
||
| padding_around_mutation : int |
There was a problem hiding this comment.
this is no longer a param here
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Outdated suggestions cannot be applied.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.
We currently have two top-level functions called
predict_epitopes_from_variantsandpredict_epitopes_from_effectswith a very large number of arguments. Creating another top-level function (e.g. to predict from protein changes without genomic variants) would require duplicating a lot of thing long argument list. To make it easier to add features in the future I'm making aTopiaryPredictorobject which holds properties shared between different top-level methods.This change is