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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Enable Users to Download Latest FASTA or XML Sequence Libraries Directly from UniProt #1937

Open trishorts opened 3 years ago

trishorts commented 3 years ago

This command works in C# to get the database.

Client.DownloadFile(@"https://www.uniprot.org/uniprot/?query=proteome:UP000005640 reviewed:yes&format=xml", @"C:\Users\h.xml");

We could make a database directory at the same level as "Mods" There is apparently a way to store the date with the file. So we can see if one needs an update. Using this date might also make the prose.txt file more data rich.

acesnik commented 3 years ago

And format=fasta&include=yes will give isoform sequences

rmillikin commented 3 years ago

this is really cool, I'd love to see this in MM

trishorts commented 3 years ago

https://www.uniprot.org/help/api%5Fqueries

trishorts commented 3 years ago

query syntax https://www.uniprot.org/help/text-search