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scverse / genomic-features

Genomic Features in Python from BioConductor's AnnotationHub
https://genomic-features.readthedocs.io
BSD 3-Clause "New" or "Revised" License
18 stars 5 forks source link

Add UCSC TxDb #66

Open gamazeps opened 3 months ago

gamazeps commented 3 months ago

Work for issue #11

This is currently a very dirty WIP, the doc is missing, the notebook is in the wrong place and will be turned into a cookbook

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codecov-commenter commented 3 months ago

Codecov Report

Attention: Patch coverage is 22.95082% with 141 lines in your changes are missing coverage. Please review.

Project coverage is 68.39%. Comparing base (a18e2fb) to head (ca0c28f). Report is 2 commits behind head on main.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #66 +/- ## =========================================== - Coverage 93.09% 68.39% -24.71% =========================================== Files 6 8 +2 Lines 333 522 +189 =========================================== + Hits 310 357 +47 - Misses 23 165 +142 ``` | [Files](https://app.codecov.io/gh/scverse/genomic-features/pull/66?dropdown=coverage&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/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/genomic-features/pull/66?src=pr&el=tree&filepath=src%2Fgenomic_features%2F__init__.py&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/ucsc/\_\_init\_\_.py](https://app.codecov.io/gh/scverse/genomic-features/pull/66?src=pr&el=tree&filepath=src%2Fgenomic_features%2Fucsc%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvdWNzYy9fX2luaXRfXy5weQ==) | `100.00% <100.00%> (ø)` | | | [src/genomic\_features/ucsc/ucscdb.py](https://app.codecov.io/gh/scverse/genomic-features/pull/66?src=pr&el=tree&filepath=src%2Fgenomic_features%2Fucsc%2Fucscdb.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse#diff-c3JjL2dlbm9taWNfZmVhdHVyZXMvdWNzYy91Y3NjZGIucHk=) | `21.66% <21.66%> (ø)` | | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/scverse/genomic-features/pull/66/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=scverse)
gamazeps commented 2 months ago

Still a massive WIP, will finish this Weekend (the bottleneck right now is finding which are the joins done to provide the tables in the R implementation)