Remove Hardcoded File Paths #211
Open
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
Only a single context can be processed at a time; if more contexts need to be processed, merge xomics should be wrapped in a for loop
There was a problem hiding this comment.
Copilot reviewed 8 out of 8 changed files in this pull request and generated no comments.
Comments suppressed due to low confidence (2)
main/como/rnaseq_gen.py:254
- Ensure that the change to avoid zero or negative values in
effective_lengthis covered by tests. If not, add tests to cover this behavior.
effective_length = [max(1e-9, size - (mean_fragment_lengths + 1)) for size in gene_size]
main/como/utils.py:163
- Ensure 'entrez_gene_id' and 'active' columns exist in expression_data before accessing them to avoid KeyError.
expression_data = expression_data[["entrez_gene_id", "active"]]
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Outdated suggestions cannot be applied.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.
Hardcoded file paths prevented using COMO as a true Python package; this removes those hardcoded items