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UniProt XML, FASTA parsers? #107

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acesnik opened this issue Mar 3, 2023 · 2 comments
Open

UniProt XML, FASTA parsers? #107

acesnik opened this issue Mar 3, 2023 · 2 comments

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@acesnik
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acesnik commented Mar 3, 2023 •
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Would it be within scope to add parsers for UniProt XML / FASTA here?
@acesnik acesnik changed the title UniProt XML / FASTA parser? UniProt XML, FASTA parsers? Mar 3, 2023
@rfellers
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rfellers commented Mar 3, 2023

I'd be up for that. We have them internally, but they aren't the best code ever. Could use a refresh. Does mzLib have these parsers?

@acesnik
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acesnik commented Mar 5, 2023

mzLib has some. They're not perfect, either, e.g., they don't create protein isoforms from XML, but they might be a place to start.

https://github.com/smith-chem-wisc/mzLib/blob/master/mzLib/UsefulProteomicsDatabases/ProteinDbLoader.cs

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