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needletail other then bio to accelerate fasta parsing #15

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jianshu93 opened this issue Nov 18, 2022 · 3 comments
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needletail other then bio to accelerate fasta parsing #15

jianshu93 opened this issue Nov 18, 2022 · 3 comments

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@jianshu93
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Hello Team,

It seems needle tail is much faster than bio for fasta file parsing. For larger fasta files, parsing can also be parallelized. Is this doable?

Thanks,

Jianshu
@suchapalaver
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Sorry for the delayed reply. I'll look into this. Thanks for the suggestion.

@suchapalaver suchapalaver mentioned this issue Dec 3, 2022
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@suchapalaver
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suchapalaver commented Dec 3, 2022 •
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@jianshu93 Check out this branch for experimenting with needletail.

@suchapalaver suchapalaver reopened this Dec 17, 2022
@suchapalaver
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@jianshu93 , I'd be interested if you think this is an improvement. I couldn't easily figure out how to parallelize processing the fasta records, what with needletail's implementation of next().

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@jianshu93 @suchapalaver