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v03_pipeline/lib/reference_data/clinvar.py

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -183,7 +183,9 @@ def download_and_import_clinvar_submission_summary() -> hl.Table:
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) as unzipped_tmp_file:
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urllib.request.urlretrieve(CLINVAR_SUBMISSION_SUMMARY_URL, tmp_file.name) # noqa: S310
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# Unzip the gzipped file first to fix gzip files being read by hail with single partition
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with gzip.open(tmp_file.name, 'rb') as f_in, open(unzipped_tmp_file.name, 'wb') as f_out:
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with gzip.open(tmp_file.name, 'rb') as f_in, open(
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unzipped_tmp_file.name, 'wb',
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) as f_out:
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shutil.copyfileobj(f_in, f_out)
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gcs_tmp_file_name = os.path.join(

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