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faster sequence file (GenBank) parsing #1

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seanrjohnson opened this issue Apr 21, 2024 · 0 comments
Open

faster sequence file (GenBank) parsing #1

seanrjohnson opened this issue Apr 21, 2024 · 0 comments
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enhancement New feature or request

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@seanrjohnson
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GenBank file parsing is a major bottleneck for domain_search.py on large databases. The current GenBank parser is a fork of the BioPython GenBank parser, which is pure python, uses some regexes, and is slow. It would be great to integrate something like the rust parser: https://github.com/althonos/gb-io.py

A complication is that Domainator internals are quite reliant on BioPython SeqRecord objects, which might be hard to interface with or replicate with a faster genbank parser.

@seanrjohnson seanrjohnson added the enhancement New feature or request label Apr 21, 2024
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