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Reduced memory demand #123

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HobnobMancer opened this issue Feb 9, 2024 · 1 comment · May be fixed by #130
Open

Reduced memory demand #123

HobnobMancer opened this issue Feb 9, 2024 · 1 comment · May be fixed by #130
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enhancement New feature or request

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@HobnobMancer
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Extremely large CAZy database releases is increasing the memory intensity of cazy_webscraper, making it difficult to run the tool on standard office equipment (see issue at cazomevovle).

The issue comes down to parsing the large CAZy text file (the CAZy db dump), and passing the data into a dict, which is memory intensive. This method needs to be changed, and broken up to reduce the computational load - ideally to below 8GB.

@HobnobMancer
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Plans for development:

  • Don't load the entire CAZy database dump into memory all at once
  • Using temp/mounting tables to reduce the amount of data that is stored in the memory
  • Transition from sqlalchemy to sqlite3

@HobnobMancer HobnobMancer linked a pull request Jun 16, 2024 that will close this issue
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