def test_compareCoordinate(self): expectedCsvRead = [ 'id', '# precursors\r\nf_43922326584371237334', '1\r\nf_130205234428175237334', '0\r\nf_8613715360396561740', '0\r\nf_13020522388175237334', '1\r\n' ] # this is the expected output of reading the output csv file expectedReturnValue = { 'totalPrecursorsInFeatures': 2, 'averagePrecursorsInFeatures': 0.5, 'featPerPrecursorDict': { 'f_13020522388175237334': 1, 'f_130205234428175237334': 0, 'f_43922326584371237334': 1, 'f_8613715360396561740': 0 } } # to make sure that the test isn't passing when the method doesn't work, but the file already exists # the file is deleted at the beginning of the test rather than at the end, because user might want to check how an example output file looks if os.path.exists(testFolder + 'testPrecursorPerFeature.csv'): os.remove(testFolder + 'testPrecursorPerFeature.csv') actualReturnValue = compare.compareCoordinate( testFolder + 'mzml_test_file_1.mzML', testFolder + 'featurexmlTestFile_1.featureXML', True, testFolder + 'testPrecursorPerFeature.csv') csvFile = open(testFolder + 'testPrecursorPerFeature.csv') csvRead = csvFile.read().split('\t') self.assertDictEqual(expectedReturnValue, actualReturnValue) self.assertListEqual(expectedCsvRead, csvRead) if os.path.exists(testFolder + 'testPrecursorPerFeature.csv'): os.remove(testFolder + 'testPrecursorPerFeature.csv')
def test_precursorPerFeatureCsvWriter(self): expectedFirstLine = ['id', '# precursors\r\n'] expectedSecondLine = {'f_43922326584371237334': 1, 'f_8613715360396561740': 0, 'f_13020522388175237334': 1} if os.path.exists(testFolder+'featPerPrecursorCsvTest.csv'): os.remove(testFolder+'featPerPrecursorCsvTest.csv') # to make sure that the test isn't passing when the method doesn't work, but the file already exists msrun = pymzml.run.Reader(testFolder+'mzml_test_file_1.mzML') precursPerFeature = compare.compareCoordinate(testFolder+'mzml_test_file_1.mzML', testFolder+'featurexmlTestFile_1.featureXML')['featPerPrecursorDict'] # see compareFeatureXMLmzML.py for details writer = output.CompareDataWriter(testFolder+'featPerPrecursorCsvTest.csv') writer.precursorPerFeatureCsvWriter(precursPerFeature) csvFile = open(testFolder+'featPerPrecursorCsvTest.csv') actualFirstLine = csvFile.readline().split('\t') actualSecondLine = csvFile.readline().split('\t') os.remove(testFolder+'featPerPrecursorCsvTest.csv')
def test_compareCoordinate(self): expectedCsvRead = ['id','# precursors\r\nf_43922326584371237334','1\r\nf_130205234428175237334','0\r\nf_8613715360396561740','0\r\nf_13020522388175237334','1\r\n'] # this is the expected output of reading the output csv file expectedReturnValue = {'totalPrecursorsInFeatures':2, 'averagePrecursorsInFeatures':0.5, 'featPerPrecursorDict':{'f_13020522388175237334': 1, 'f_130205234428175237334': 0, 'f_43922326584371237334': 1, 'f_8613715360396561740': 0}} # to make sure that the test isn't passing when the method doesn't work, but the file already exists # the file is deleted at the beginning of the test rather than at the end, because user might want to check how an example output file looks if os.path.exists(testFolder+'testPrecursorPerFeature.csv'): os.remove(testFolder+'testPrecursorPerFeature.csv') actualReturnValue = compare.compareCoordinate(testFolder+'mzml_test_file_1.mzML', testFolder+'featurexmlTestFile_1.featureXML', True, testFolder+'testPrecursorPerFeature.csv') csvFile = open(testFolder+'testPrecursorPerFeature.csv') csvRead = csvFile.read().split('\t') self.assertDictEqual(expectedReturnValue, actualReturnValue) self.assertListEqual(expectedCsvRead, csvRead) if os.path.exists(testFolder+'testPrecursorPerFeature.csv'): os.remove(testFolder+'testPrecursorPerFeature.csv')
def test_precursorPerFeatureCsvWriter(self): expectedFirstLine = ['id', '# precursors\r\n'] expectedSecondLine = { 'f_43922326584371237334': 1, 'f_8613715360396561740': 0, 'f_13020522388175237334': 1 } if os.path.exists(testFolder + 'featPerPrecursorCsvTest.csv'): os.remove( testFolder + 'featPerPrecursorCsvTest.csv' ) # to make sure that the test isn't passing when the method doesn't work, but the file already exists msrun = pymzml.run.Reader(testFolder + 'mzml_test_file_1.mzML') precursPerFeature = compare.compareCoordinate( testFolder + 'mzml_test_file_1.mzML', testFolder + 'featurexmlTestFile_1.featureXML' )['featPerPrecursorDict'] # see compareFeatureXMLmzML.py for details writer = output.CompareDataWriter(testFolder + 'featPerPrecursorCsvTest.csv') writer.precursorPerFeatureCsvWriter(precursPerFeature) csvFile = open(testFolder + 'featPerPrecursorCsvTest.csv') actualFirstLine = csvFile.readline().split('\t') actualSecondLine = csvFile.readline().split('\t') os.remove(testFolder + 'featPerPrecursorCsvTest.csv')