Refactor branch #6
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- Fixed ValueError return for mutliple HGNC_ids - Updated merge_overlapping function to return correct df according to docstring. - Moved order in write_bed so collapsing is done after combining coordinates_df and annotation_df. -Write_bed also returns the correct empty df now. -Removed some lines from write_bed into merge_overlapping to make consistent. - Added additional example cmd to script docstring Tests added: - Test for empty annotation_df and correct results. - Test am error is raised for multiple hgnc ids. - Test correct merged_overlapping coordinates returned.
…ecting only NM_ transcripts, this might be removed on consultation. Added section explaining how to use this with VEP. Added example of gff3 tsv.
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Hello @RSWilson1! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
Comment last updated at 2024-02-19 09:45:44 UTC |
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Reviewed 2 of 4 files at r1, 2 of 2 files at r2, all commit messages.
Reviewable status:complete! all files reviewed, all discussions resolved (waiting on @RSWilson1)
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Added changes to cover more with tests and change functionality of some code:
annotation_dfand move code to fit into functions better.annotation_dfandcoordinates_df.This change is