Validity check v4 exomes #487
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Loggers seem to not be working for me right now |
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Loggers are a gnomad_methods issue: https://the-tgg.slack.com/archives/C6BD1M01E/p1697463923095569 |
…to mw/validity_check_v4_exomes # Conflicts: # gnomad_qc/v4/resources/release.py
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I think this is looking good, I only looked at it for logic, which is totally fine at this point.
I think we might want to add in some other checks, like a check for length of globals being the expected length, and maybe counts being the expected counts. Maybe check for any uses of 'pop' or 'oth' in the globals?
Are there any other checks that we thing should be done on the globals? @ch-kr ?
Then only a few small suggestions
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I've updated this and it depends on broadinstitute/gnomad_methods#630. In the |
| NEW_SITE_FIELDS = [ | ||
| "monoallelic", | ||
| "only_het", | ||
| "transmitted_singleton", |
| from gnomad_qc.v4.resources.basics import get_logging_path | ||
| from gnomad_qc.v4.resources.release import release_sites, validated_release_ht | ||
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| # TODO: Check global lengths match the fields they reference |
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| # TODO: Check global lengths match the fields they reference |
| "release_ht": [ | ||
| "gs://gnomad-tmp/gnomad.exomes.v4.0.qc_data/release/gnomad.exomes.sites.test.updated_101723.ht" | ||
| ] | ||
| }, # release_sites().ht()}, |
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I know this is just for testing, but don't forget to change it back
| return vep_csq_header | ||
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| def check_globals_for_retired_terms(ht: hl.Table) -> None: |
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This is great, thank you!!
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Back to you @jkgoodrich -- agree on seeing the output of the globals and len checks as confirmations, good call on adding those |
Co-authored-by: jkgoodrich <[email protected]>
This unfurls and runs gnomad_methods validate_release_t on the v4 exomes release HT. It depends on broadinstitute/gnomad_methods#625 and there is some room for improvements but I just wanted to get it in. It writes out the HT with unfurled annotations that will move to the next step.