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Pr/5 #8

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more tests
  • Loading branch information
ypriverol committed Aug 3, 2021
commit ddbd9b07198bfa1a9cf23d828fd744ad8a38b796
6 changes: 0 additions & 6 deletions src/main/java/de/mpc/pia/modeller/exporter/MzTabExporter.java
Original file line number Diff line number Diff line change
@@ -910,12 +910,6 @@ private ParamList preprocessAdditionalParams(ParamList paramList, Metadata mtd)
}
}

/*
// TODO: process userParams
for (UserParam param : paramList.getUserParam()) {
}
*/

return unprocessedParams;
}

Original file line number Diff line number Diff line change
@@ -4,7 +4,6 @@
import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;

Original file line number Diff line number Diff line change
@@ -55,33 +55,6 @@ public void getDataFromPrideXMLFileTest() throws IOException {

compiler.writeOutXML(piaIntermediateFile);
compiler.finish();

/*
PIAModeller piaModeller = new PIAModeller(piaIntermediateFile.getAbsolutePath());

// PSM level
piaModeller.setCreatePSMSets(true);
assertEquals("createPSMSets should be true", true, piaModeller.getCreatePSMSets());

piaModeller.getPSMModeller().setAllDecoyPattern(FDRData.DecoyStrategy.SEARCHENGINE.toString());

piaModeller.getPSMModeller().calculateAllFDR();
piaModeller.getPSMModeller().calculateCombinedFDRScore();

SpectrumExtractorInference seInference = new SpectrumExtractorInference();

seInference.addFilter(new PSMScoreFilter(FilterComparator.less_equal, false, 0.01, ScoreModelEnum.PSM_LEVEL_COMBINED_FDR_SCORE.getShortName()));

seInference.setScoring(new MultiplicativeScoring(new HashMap<String, String>()));
seInference.getScoring().setSetting(AbstractScoring.scoringSettingID, ScoreModelEnum.PSM_LEVEL_COMBINED_FDR_SCORE.getShortName());
seInference.getScoring().setSetting(AbstractScoring.scoringSpectraSettingID, PSMForScoring.ONLY_BEST.getShortName());

piaModeller.getProteinModeller().infereProteins(seInference);

List<ReportProtein> proteins = piaModeller.getProteinModeller().getFilteredReportProteins(null);

Assert.assertTrue(reader.getIdentIds().size() - 1 == proteins.size());
*/
}

}
48 changes: 0 additions & 48 deletions src/test/java/de/mpc/pia/modeller/SerializationTest.java
Original file line number Diff line number Diff line change
@@ -163,13 +163,6 @@ public void testSerializingCustom() throws IOException {

}

/*
LOGGER.debug("object: "
+ piaModeller.getPSMModeller().getEvilData().get(new Long(14))
.getSpectrum().getSequence()
);
*/

piaModeller = new PIAModeller();

PIAModeller readModel;
@@ -199,46 +192,5 @@ public void testSerializingCustom() throws IOException {
e.printStackTrace();
throw new IOException(msg, e);
}


/*
// reading in the serialized object
piaModeller = PIAModeller.deSerializeFromFile(serialFile);

assertEquals("ProjectName is not correct", "testfile", piaModeller.getProjectName());
assertEquals("number of files in PIA XML is not correct", 2, piaModeller.getFiles().size());

assertEquals("createPSMSets should be true", true, piaModeller.getCreatePSMSets());

assertEquals("Decoy pattern wrong", "Rnd.*", piaModeller.getPSMModeller().getFilesFDRData(1L).getDecoyPattern());
assertEquals("Decoy pattern wrong", "Rnd.*", piaModeller.getPSMModeller().getFilesFDRData(2L).getDecoyPattern());

assertEquals("number of PSM sets is wrong", 2426, piaModeller.getPSMModeller().getNrReportPSMs(0L));
assertEquals("number of PSMs in file 1 is wrong", 2308, piaModeller.getPSMModeller().getNrReportPSMs(1L));
assertEquals("number of PSMs in file 2 is wrong", 170, piaModeller.getPSMModeller().getNrReportPSMs(2L));


assertEquals("wrong preferred FDR score", "mascot_expect",
piaModeller.getPSMModeller().getPreferredFDRScores().get(0));

assertEquals("number of filtered PSM sets is wrong", 8,
piaModeller.getPSMModeller().getFilteredReportPSMSets(piaModeller.getPSMModeller().getFilters(0L)).size());

assertEquals("number of filtered protein groups is wrong", 6,
piaModeller.getProteinModeller().getFilteredReportProteins(null).size());


assertEquals("Wrong inference method", "Spectrum Extractor",
piaModeller.getProteinModeller().getAppliedProteinInference().getName());

assertEquals("Wrong scoring method", MultiplicativeScoring.NAME,
piaModeller.getProteinModeller().getAppliedProteinInference().getScoring().getName());

assertEquals("Wrong number of filters", 1,
piaModeller.getProteinModeller().getAppliedProteinInference().getFilters().size());

assertEquals("Wrong filter", FilterComparator.less_equal,
piaModeller.getProteinModeller().getAppliedProteinInference().getFilters().get(0).getFilterComparator());
*/
}
}
Original file line number Diff line number Diff line change
@@ -35,8 +35,6 @@ public class MzTabExporterForPRIDEReanalysisTest {

@Before
public void setUp() {
//piaFile = new File("/mnt/data/uniNOBACKUP/PIA/PXD001428/PXD001428_0.pia.xml");
//piaFile = new File("/mnt/data/uniNOBACKUP/PIA/PRD000397/PRD000397.pia.xml");
piaFile = new File("/mnt/data/uniNOBACKUP/PIA/PXD001428/OR8_130622_TT_Trypsin_Ti-IMAC_Rep1_B1[Node_05].scored.pia.xml");
}

Original file line number Diff line number Diff line change
@@ -45,14 +45,7 @@ public void testMzTabExporter() throws IOException {
// they are erronous in PRIDE XML
psmSetSettings.remove(IdentificationKeySettings.SOURCE_ID.toString());


// not available in this case
//psmSetSettings.remove(IdentificationKeySettings.RETENTION_TIME.toString());
//psmSetSettings.remove(IdentificationKeySettings.SPECTRUM_TITLE.toString());


piaModeller.getPSMModeller().setPSMSetSettings(psmSetSettings);

piaModeller.getPSMModeller().applyGeneralSettings(true);

piaModeller.getPSMModeller().setAllDecoyPattern(FDRData.DecoyStrategy.SEARCHENGINE.toString());
Original file line number Diff line number Diff line change
@@ -95,22 +95,6 @@ public void testPIASearchEngineFilterAndAnalysis() throws IOException {

Assert.assertEquals(4510, psmSets.size());


/*
// protein level
SpectrumExtractorInference seInference = new SpectrumExtractorInference();

seInference.setScoring(new MultiplicativeScoring(new HashMap<>()));
seInference.getScoring().setSetting(AbstractScoring.SCORING_SETTING_ID, ScoreModelEnum.PSM_LEVEL_FDR_SCORE.getShortName());
seInference.getScoring().setSetting(AbstractScoring.SCORING_SPECTRA_SETTING_ID, PSMForScoring.ONLY_BEST.getShortName());

piaModeller.getProteinModeller().infereProteins(seInference);

piaModeller.getProteinModeller().updateFDRData(DecoyStrategy.ACCESSIONPATTERN, "s.*", 0.01);
piaModeller.getProteinModeller().updateDecoyStates();
piaModeller.getProteinModeller().calculateFDR();
*/

piaIntermediateFile.delete();
}