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')