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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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[FEATURE] merge same run #50

Closed hroest closed 5 years ago

hroest commented 5 years ago

We have some data in our lab where we are running overlapping windows and each mzML file produces 2 .osw files since we need to split the files and run them separately through OpenSWATH. This PR allows merging of the two files again but treating them as coming from the same original file. This is important because we may have duplicate entries (e.g. tr_gr_1 was extracted from both OpenSWATH runs but we want to score them together so that tr_gr_1 gets selected only once, either from osw_1 or from osw_2). I think this PR should allow that, any feedback?

grosenberger commented 5 years ago

I think that makes a lot of sense. One option would be to remove the parameter and merge with this scheme if the file names are the same. But this might add confusion if mistakenly the same OSW is merged twice.

Feel free to merge when ready.

hroest commented 5 years ago

One option would be to remove the parameter and merge with this scheme if the file names are the same.

I think its better to be explicit about this, leads to less confusion and "surprises"