Add find missing genes function and update gene map#11
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Pull request overview
This PR adds a new public method find_missing_genes() to the UploadValidator class to help users identify genes in their AnnData files that are missing from the gene map. The implementation refactors existing validation logic to return missing gene information.
Key changes:
- Added
find_missing_genes()public method that returns a DataFrame of missing genes - Refactored
_check_var_index()and_validate_gene_ids()to return boolean masks of missing genes instead of just validating - Added
Uniontype hint import for optional return values
Reviewed changes
Copilot reviewed 2 out of 3 changed files in this pull request and generated 7 comments.
| File | Description |
|---|---|
| src/cap_upload_validator/upload_validator.py | Added new find_missing_genes() method and refactored validation methods to return missing gene masks while maintaining backward compatibility with validation flow |
| CHANGELOG.md | Documented the new find_missing_genes() function and gene map updates |
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