def testExtentOutOfRangeError(self):
''' If a window is specified that extends beyond the beginning or end of a file, truncate the ref_context.
Use what is left for gc_content as well.'''
ds = ReferenceDatasource('testdata/reference_ds',
windowSizeRef=6,
windowSizeGCContent=5)
m = MutationDataFactory.default_create()
m.chr = "22"
m.start = "4"
m.end = "4"
# "CCCAAGCTAAACCCAGGCCAC"
groundTruth = "CCCAAGCTAA"
guess = ds.annotate_mutation(m)
self.assertTrue(
guess['ref_context'] == groundTruth,
"ref_context was not populated properly: " +
str(guess['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(
fabs(float(guess['gc_content']) - (float(5) / float(9))) < .001,
"gc_content was not populated properly: " +
str(guess['gc_content']))
def testEmptyAnswer(self):
''' The Reference Datasource should return a blank result if the chromosome is not found.
Note: A log entry should also be written, but this is not tested. '''
self.logger.info("Please ignore the next logging warning: testdata/reference_ds/chrTHIS_DOES_NOT_EXIST.txt not found. Please add it.")
ds = ReferenceDatasource('testdata/reference_ds')
m = MutationDataFactory.default_create()
m.chr = "THIS_DOES_NOT_EXIST"
m.start = "11"
m.end = "11"
groundTruth = ""
# remember that the annotate_mutation returns a generator, so we use an iterator
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly -- should be blank: " + str(guess['ref_context']))
def testEmptyAnswer(self):
''' The Reference Datasource should return a blank result if the chromosome is not found.
Note: A log entry should also be written, but this is not tested. '''
self.logger.info("Please ignore the next logging warning: testdata/reference_ds/chrTHIS_DOES_NOT_EXIST.txt not found. Please add it.")
ds = ReferenceDatasource('testdata/reference_ds')
m = MutationData()
m.chr = "THIS_DOES_NOT_EXIST"
m.start = "11"
m.end = "11"
groundTruth = ""
# remember that the annotate_mutation returns a generator, so we use an iterator
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly -- should be blank: " + str(guess['ref_context']))
def testSimpleGLAnnotate(self):
''' Test a simple annotation case. Make sure that the ref_context and gc_content annotations are correct. '''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeGCContent=5)
m = MutationDataFactory.default_create()
m.chr = "GL000211.1"
m.start = "11"
m.end = "11"
groundTruth = "gaattctttttcaagtaagtc"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(m['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content']) - (float(3)/float(11))) < .001, "gc_content was not populated properly: " + str(m['gc_content']))
def testSimpleGLAnnotate(self):
''' Test a simple annotation case. Make sure that the ref_context and gc_content annotations are correct. '''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeGCContent=5)
m = MutationData()
m.chr = "GL000211.1"
m.start = "11"
m.end = "11"
groundTruth = "gaattctttttcaagtaagtc"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(m['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content']) - (float(3)/float(11))) < .001, "gc_content was not populated properly: " + str(m['gc_content']))
def testSimpleAnnotate(self):
''' Perform a simple test of one of the aligned chromosomes (chr22) and make sure that we get a reasonable answer.
'''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeGCContent=5)
m = MutationDataFactory.default_create()
m.chr = "22"
m.start = "11"
m.end = "11"
groundTruth = "CCCAAGCTAAACCCAGGCCAC"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(guess['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content'])- (float(6)/float(11))) < .001, "gc_content was not populated properly: " + str(guess['gc_content']))
def testSimpleAnnotate(self):
''' Perform a simple test of one of the aligned chromosomes (chr22) and make sure that we get a reasonable answer.
'''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeGCContent=5)
m = MutationData()
m.chr = "22"
m.start = "11"
m.end = "11"
groundTruth = "CCCAAGCTAAACCCAGGCCAC"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(guess['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content'])- (float(6)/float(11))) < .001, "gc_content was not populated properly: " + str(guess['gc_content']))
def testExtentOutOfRangeError(self):
''' If a window is specified that extends beyond the beginning or end of a file, truncate the ref_context.
Use what is left for gc_content as well.'''
ds = ReferenceDatasource('testdata/reference_ds', windowSizeRef=6, windowSizeGCContent=5)
m = MutationDataFactory.default_create()
m.chr = "22"
m.start = "4"
m.end = "4"
# "CCCAAGCTAAACCCAGGCCAC"
groundTruth = "CCCAAGCTAA"
guess = ds.annotate_mutation(m)
self.assertTrue(guess['ref_context'] == groundTruth, "ref_context was not populated properly: " + str(guess['ref_context']))
# gc_content is rounded to 3 decimal places
self.assertTrue(fabs(float(guess['gc_content']) - (float(5)/float(9))) < .001, "gc_content was not populated properly: " + str(guess['gc_content']))