Fix xpath, improve pepxml.roc_curve()

levitsky / pyteomics

Pyteomics is a collection of lightweight and handy tools for Python that help to handle various sorts of proteomics data. Pyteomics provides a growing set of modules to facilitate the most common tasks in proteomics data analysis.

http://pyteomics.readthedocs.io

Apache License 2.0

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Fix xpath, improve pepxml.roc_curve() #10

Closed alephreish closed 4 years ago

alephreish commented 4 years ago

Fixes xpath bugs in pepxml.roc_curve() that caused a fatal error [XPathEvalError: Invalid predicate]
Adds "charge" and "tag" keys to the output to make the function usable in real world.

levitsky commented 4 years ago

Thank you! This is a legacy function and to be honest I don't think I've ever used it myself. One minor question: should we maybe convert charge to an integer?

alephreish commented 4 years ago

Hi! I wrote my own parser for pepxml in node.js, but recently decided to switch to pyteomics for everyday use - that's when I discovered also roc_curve(). No, "charge" has to remain string as it is a categorical variable and will be used as such in most of the cases. It goes: "all", "2", "3" and "4".

levitsky commented 4 years ago

Ah, OK, thanks.

I'm glad you've found pyteomics to be of use and thank you for the contribution!