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TODO: add note for future work
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  • data-pipeline/src/data_pipeline/datasets

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data-pipeline/src/data_pipeline/datasets/clinvar.py

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@@ -202,7 +202,8 @@ def parse_clinvar_xml_to_tsv(
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with open_function(input_xml_path, "r") as xml_file:
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# The exact number of variants in the XML file is unknown.
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# Approximate it to show a progress bar.
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progress = tqdm(total=3_100_000, mininterval=5)
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# TODO: approximate this using filesize instead?
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progress = tqdm(total=4_000_000, mininterval=5)
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xml = ElementTree.iterparse(xml_file, events=["end"])
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for _, element in xml:
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if element.tag == "ClinVarVariationRelease":

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