scverse / genomic-features

Genomic Features in Python from BioConductor's AnnotationHub
https://genomic-features.readthedocs.io
BSD 3-Clause "New" or "Revised" License
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Add gene annotations to anndata vars #23

Open emdann opened 1 year ago

emdann commented 1 year ago

Closes #14

codecov-commenter commented 1 year ago

Codecov Report

Merging #23 (e669b8b) into main (2398977) will decrease coverage by 0.98%. The diff coverage is 92.98%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #23 +/- ## ========================================== - Coverage 93.69% 92.72% -0.98% ========================================== Files 6 7 +1 Lines 333 371 +38 ========================================== + Hits 312 344 +32 - Misses 21 27 +6 ``` | [Impacted Files](https://app.codecov.io/gh/scverse/genomic-features/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse) | Coverage Δ | | |---|---|---| | [src/genomic\_features/annotate.py](https://app.codecov.io/gh/scverse/genomic-features/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvYW5ub3RhdGUucHk=) | `89.18% <89.18%> (ø)` | | | [src/genomic\_features/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/genomic-features/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [src/genomic\_features/ensembl/ensembldb.py](https://app.codecov.io/gh/scverse/genomic-features/pull/23?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvZW5zZW1ibC9lbnNlbWJsZGIucHk=) | `93.15% <100.00%> (-1.06%)` | :arrow_down: |
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emdann commented 1 year ago

Outstanding issues:

lauradmartens commented 1 year ago

Looks good! I added a few minor comments :)

emdann commented 1 year ago

@ivirshup wrt Ensembl version matching, the pbmc3k data was mapped with cellranger 1.1, but I am having a hard time matching this version to a Ensembl release.

I'm gonna use the data from scvi.data.heart_cell_atlas_subsampled which is mapped to cellranger 3.0.1 with hg38 which according to the old release notes corresponds to Ensembl release 93.