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Parallelise combine scorefiles #43

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nebfield opened this issue Aug 5, 2024 · 0 comments
Open

Parallelise combine scorefiles #43

nebfield opened this issue Aug 5, 2024 · 0 comments
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enhancement New feature or request

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@nebfield
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nebfield commented Aug 5, 2024 •
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It's currently bottlenecked by creating millions of python objects (ScoreVariants, one per row). Should be pretty simple to implement. Just need to:

  • Write each normalised scoring file to a new corresponding file (currently all files are written to a single combined file)
  • Change output from csv.gz to arrow (ipc) to support lazy scanning by pgscatalog-match
  • Set up a process pool executor to distribute jobs to worker processes in the CLI
@nebfield nebfield added the enhancement New feature or request label Aug 5, 2024
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