Comments (2)
ericminikel
commented on July 19, 2024
Thanks @gturenchalk (and thanks to @bw2 who also pointed this out and talked through solutions with me). I have now switched to iterparse as of this commit and it appears to be working.
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ericminikel
commented on July 19, 2024
Turns out I forgot to add elem.clear() on my first go; I have now added it and successfully ran parse_clinvar_xml.py to completion in under a half hour (used to take 3 hours). I didn't explicitly check peak memory usage but I was able to run it on an interactive node which I couldn't before, so I believe it is much lower.
I will close this issue for now but feel free to re-open if you find that you still have trouble.
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Related Issues (20)
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