Add support for pepxml files with search_engine = Percolator #3278
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… code to PepXMLReader to handle this
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Thanks for the PR. It needs a test added though. Easiest way would be taking one of the existing Percolated pepXMLs and changing the search_engine (and removing post-processor parameter if OpenMS doesn't set that). Better would be getting a real OpenMS pepXML but cutting it down to be <1MB. Is it clear enough how to add a test when looking at the tests/Jamfile.jam? (when you run the test the first time it will create a reference/xxx.observed file; just change that .check after reviewing it to be sure it's correct and then the test should pass).
| @@ -419,7 +426,8 @@ void PepXMLreader::startElement(const XML_Char* name, const XML_Char** attr) | |||
| (analysisType_ == PROTEOME_DISCOVERER_ANALYSIS && scoreType_ == MASCOT_IONS_SCORE && score_name == "exp-value") || | |||
| (analysisType_ == MORPHEUS_ANALYSIS && score_name == "psm q-value") || | |||
| (analysisType_ == MSGF_ANALYSIS && score_name == "qvalue") || | |||
| (analysisType_ == CRUX_ANALYSIS && score_name == "percolator_qvalue")) { | |||
| (analysisType_ == CRUX_ANALYSIS && score_name == "percolator_qvalue") | |||
| (analysisType_ == PERCOLATOR_ANALYSIS)) { | |||
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Looks like a missing || operator? How did this work?
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And this is why I shouldnt push changes on a friday afternoon. Fixed.
I've been working on the test for this, a meaningful search with decoys, in a small mzml file, that produces better results than "nothing found" is proving to be a pain. I'm not going to have a chance to circle back to this before the holidays, so I'm putting a note in my calendar to come back in early Jan. |
OpenMS' Percolator adapter saves the search_engine as Percolator directly. As a result it's not possible to load OpenMS generated pepxmls that have Percolator postprocessing into Skyline. This patch fixes that.