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medbioinf / pia

:books: :microscope: PIA - Protein Inference Algorithms
https://github.com/medbioinf/pia
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CSV format for PSM results as input file #163

Open cctsou opened 3 years ago

cctsou commented 3 years ago

Hi,

Does PIA accept PSM result input in simple TSV / CSV format? If yes, what does the format look like?

Thanks,

julianu commented 3 years ago

Hej @cctsou ,

PIA currently supports using files created by Tide, see e.g. https://github.com/mpc-bioinformatics/pia/blob/master/src/test/resources/tide-search-cut.txt

If you can bring your CSV in this format, you should be able to parse them with PIA.

Best, Julian

julianu commented 2 years ago

Hej @cctsou ,

Could you solve your problem?

Best, Julian

mcburke-msdc commented 2 years ago

I have formatted PSM results using the Tide example provided, but I have not been able to parse them with PIA within knime. In particular, I am unsure of how to configure PIA Compiler. What changes should be made to the configuration compared to providing input in idXML format?

Thank you.

julianu commented 10 months ago

Hej @mcburke-msdc , The tide and CSV parsing seems to need an update, but do you actually still have this issue (apologies for the very late answer).