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pymzml / pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files
https://pymzml.readthedocs.io/en/latest/
MIT License
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run.Reader can't handle mzML's with UV data #119

Closed pyeguy closed 5 years ago

pyeguy commented 5 years ago

I frequently have mzML chromatograms w/ UV data associated with them. This registers as a spec w/ ms_level as 0 which throws a KeyError when doing the ms_precisions look up.

I'm going to submit a pull request that adds a 0 key w/ an arbitrary precision of 0.001 which i use to fix this issue locally. Let me know if that default value should be higher or lower in your opinion.

pyeguy commented 5 years ago

added #120 to address this

MKoesters commented 5 years ago

Hi and thanks for reporting this, I personally have never worked with UV data, so I cant say what a reasonable default would look like. Since this is just a minor change without to much implications (I hope) I'll just accept your pull request. But I'll have a look at this kind of data more closely in the next week, since I'm traveling a lot currently and I'm a bit short on time for open source projects.

Best, Manuel

pyeguy commented 5 years ago

Sounds good, I'm not sure what the precision is for most diode array UV abs detectors. I can do some poking around and see if there are some common manufacturer stats that could be averaged for a reasonable default.