Suggestions on the initial toolbox PR #5
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- Add a description of the repo structure to the README - Add some potential requirements - Update the documentation and make sure it works - Create a notebook specific to loading gnomAD release data and just showing what each dataset looks like.
- Add a description of the repo structure to the README - Add some potential requirements - Update the documentation and make sure it works - Create a notebook specific to loading gnomAD release data and just showing what each dataset looks like.
- Addition of variant.py to store some functions that can also be used by frequency based filtering - Changes to frequency filtering to use new default settings if not passed a ht
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| │ ├── intro_to_release_data.ipynb # Jupyter notebook introducing the loading of gnomAD release data. | ||
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| # TODO: Add fully detailed info about how to install and open the notebooks. |
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These steps should include:
- install miniconda;
- set up a conda env for a specific version of Hail (and update JAVA);
- pip install gnomad_toolbox;
- set up the service account;
I can write this part once your PR is merged into mine.
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Sounds good, but don't add anything yet. First step is to get a bunch of tickets in for todo's and we can decide who will tackle what
| hl.utils.warning( | ||
| f"No variant found at {variant.locus} with alleles {variant.alleles}" | ||
| ) |
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This warning is not working. Should we use import warnings instead?
Could be:
warnings.warn(
f"No variant found at {variant.locus} with alleles {variant.alleles}",
RuntimeWarning,
)
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really? I got the warning
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Yeah, it's working, but it was printed after the init cell. 
I didn't see it because I was far down the notebook.
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| # TODO: Consider this alternative approach to get the intervals from gencode. That |
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I think your way is good, only a tiny problem, the gencode the Browser team used was preprocessed, I think they filtered out genes with the same ENSG that appear on both chrX and chrY (46 of them: 26 PAR, overlapping locus etc). We will get a different number of variants for those genes, e.x. https://gnomad.broadinstitute.org/gene/ENSG00000196433?dataset=gnomad_r4.
Do we want to add a prefilter function or just add a note?
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OK, lets go with the faster way and a filter so we get the same numbers as the browser would get. For now lets just add a TODO and a ticket to do it
Co-authored-by: Qin He <44242118+KoalaQin@users.noreply.github.com>
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