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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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tandem.DataFrame fails when tandem was run on .cmn input #74

Closed kesinger closed 2 years ago

kesinger commented 2 years ago

When x!tandem is run on a file in 'common' format (https://www.thegpm.org/common/index.html) it appears to produce slightly different XML. In particular, there is no 'note' tag inside the 'fragment ion mass spectrum', so the access here: https://github.com/levitsky/pyteomics/blob/master/pyteomics/tandem.py#L326 fails.

If I use tandem.read instead, it appears to work.

levitsky commented 2 years ago

Thanks for reporting! If you can try the latest master, hopefully the issue is solved.

kesinger commented 2 years ago

Seems to work. Thanks!