@tests: FeatureXMLFile FeatureXMLFile.__init__ FeatureXMLFile.load FeatureXMLFile.store FeatureXMLFile.getOptions FeatureXMLFile.setOptions FeatureXMLFile.loadSize FileHandler.__init__ FileHandler.loadFeature
()
| 2045 | |
| 2046 | @report |
| 2047 | def testFeatureXMLFile(): |
| 2048 | """ |
| 2049 | @tests: FeatureXMLFile |
| 2050 | FeatureXMLFile.__init__ |
| 2051 | FeatureXMLFile.load |
| 2052 | FeatureXMLFile.store |
| 2053 | FeatureXMLFile.getOptions |
| 2054 | FeatureXMLFile.setOptions |
| 2055 | FeatureXMLFile.loadSize |
| 2056 | |
| 2057 | FileHandler.__init__ |
| 2058 | FileHandler.loadFeature |
| 2059 | """ |
| 2060 | |
| 2061 | fm = pyopenms.FeatureMap() |
| 2062 | fm.setUniqueIds() |
| 2063 | |
| 2064 | f = pyopenms.Feature() |
| 2065 | f.setMZ(200) |
| 2066 | f.setCharge(1) |
| 2067 | f.setRT(10) |
| 2068 | f.setIntensity(10000) |
| 2069 | f.setOverallQuality(10) |
| 2070 | |
| 2071 | ch = pyopenms.ConvexHull2D() |
| 2072 | ch.setHullPoints(np.asarray([[8,199],[12,201]], dtype='f')) |
| 2073 | f.setConvexHulls([ch]) |
| 2074 | |
| 2075 | f.setMetaValue(b'mv1', 1) |
| 2076 | f.setMetaValue(b'mv2', 2) |
| 2077 | |
| 2078 | f.setMetaValue('spectrum_native_id', 'spectrum=123') |
| 2079 | pep_id = pyopenms.PeptideIdentification() |
| 2080 | pep_id.insertHit(pyopenms.PeptideHit()) |
| 2081 | f.setPeptideIdentifications([pep_id]) |
| 2082 | |
| 2083 | fm.push_back(f) |
| 2084 | |
| 2085 | f.setMetaValue('spectrum_native_id', 'spectrum=124') |
| 2086 | fm.push_back(f) |
| 2087 | |
| 2088 | assert len(fm.get_assigned_peptide_identifications()) == 2 |
| 2089 | assert fm.get_df(meta_values='all').shape == (2, 16) |
| 2090 | assert fm.get_df(meta_values='all', export_peptide_identifications=False).shape == (2, 12) |
| 2091 | |
| 2092 | assert pd.merge(fm.get_df(), pyopenms.peptide_identifications_to_df(fm.get_assigned_peptide_identifications()), |
| 2093 | on = ['feature_id', 'ID_native_id', 'ID_filename']).shape == (2,24) |
| 2094 | |
| 2095 | fm = pyopenms.FeatureMap() |
| 2096 | pyopenms.FeatureXMLFile().load(os.path.join(os.environ['OPENMS_DATA_PATH'], 'examples/FRACTIONS/BSA1_F1_idmapped.featureXML'), fm) |
| 2097 | |
| 2098 | assert pd.merge(fm.get_df(), pyopenms.peptide_identifications_to_df(fm.get_assigned_peptide_identifications()), |
| 2099 | on = ['feature_id', 'ID_native_id', 'ID_filename']).shape == (15,26) |
| 2100 | |
| 2101 | fh = pyopenms.FeatureXMLFile() |
| 2102 | fh.store("test.featureXML", fm) |
| 2103 | fh.load("test.featureXML", fm) |
| 2104 |
nothing calls this directly
no test coverage detected