Add import code for GTEx v10 RSEM #742
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| from gnomad.utils.vep import vep_or_lookup_vep | ||
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| def _import_gtex_rsem(gtex_path: str, meta_path: str, **kwargs) -> hl.MatrixTable: |
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Is this exactly the same as the one in grch37? If so, we should probably just import it from there
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It is, I just wonder if you used this function to get that MT, it seems the same structure as I see in the MT.
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also because it's giving a warning this underscore named function: access to a protected member * of a module
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Yeah, don't worry about the warning, or remove the _. Let me confirm, but I think it's the same function
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I did this
from gnomad.resources.grch37.reference_data import _import_gtex_rsem
try:
mt = hl.read_matrix_table("gs://gnomad/resources/grch38/gtex/gtex_rsem_v10.mt")
except:
mt = _import_gtex_rsem(
gtex_path="gs://gnomad/resources/gtex/v10/GTEx_Analysis_2022-06-06_v10_RSEMv1.3.3_transcripts_tpm.txt.bgz",
meta_path="gs://gnomad/resources/gtex/v10/GTEx_Analysis_v10_Open_Access_Reduced_Annotations_SampleAttributesDS.txt.bgz",
min_partitions=1000,
).checkpoint("gs://gnomad/resources/grch38/gtex/gtex_rsem_v10.mt", _read_if_exists=True)
gnomad/utils/filtering.py
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| "This Gencode CDS interval filter does not filter by transcript! Please see the" | ||
| " documentation for more details to confirm it's being used as intended." | ||
| ) | ||
| if padding: |
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Maybe put this in another PR since it's not related to the resource
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ah, sorry, this might be from my work on the toolbox, I wanted to modify this function at the beginning then Riley told me their function to get the CDS, I didn't look into the difference, but I did find the reason for the difference, and I commented on your toolbox PR.
This copies the import function as for GRCh37 v7, but modified a bit according the current path.