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Protein sequence (with optional alphabets) support / FFI #23

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olgabot opened this issue Mar 15, 2024 · 0 comments
Open

Protein sequence (with optional alphabets) support / FFI #23

olgabot opened this issue Mar 15, 2024 · 0 comments

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@olgabot
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olgabot commented Mar 15, 2024

Hello,
Hope you are doing well. I have used degenerate protein alphabets to another k-mer based program, Sourmash, specifically the Dayhoff table and Hydrophobic-Polar table.

I'd love to test SPLASH vs Sourmash on UniProt protein sequences, but I saw that in splash.py, there's no foreign function interface (FFI) used in Python, it's all sys calls. Is there a way I can call splash.consume_sequence(seq) or something? I'd like to run on a stream of strings created from REST API calls to UniProt, so the fasta parsing wouldn't work as well for me.
Thank you so much!
Warmest,
Olga

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