def testNotOffline(self):
"""
If the sequence fetcher does not return C{None} we must be marked as
being online.
"""
def fetcher(title, db='database'):
return SeqRecord(None)
featureList = FeatureList('title', 'database', set(),
sequenceFetcher=fetcher)
self.assertEqual(False, featureList.offline)
def testNoFeaturesLength(self):
"""
If the sequence fetcher returns a record with no features, the
L{FeatureList} instance must have length zero.
"""
def fetcher(title, db='database'):
return SeqRecord(None)
featureList = FeatureList('title', 'database', set(),
sequenceFetcher=fetcher)
self.assertEqual(0, len(featureList))
def testOfflineLength(self):
"""
If the sequence fetcher indicates we're offline, the feature list
must have length zero.
"""
def fetcher(title, db='database'):
return None
featureList = FeatureList('title', 'database', set(),
sequenceFetcher=fetcher)
self.assertEqual(0, len(featureList))
def testOffline(self):
"""
If the sequence fetcher returns C{None} we must be marked as being
offline.
"""
def fetcher(title, db='database'):
return None
featureList = FeatureList('title', 'database', set(),
sequenceFetcher=fetcher)
self.assertEqual(True, featureList.offline)
def testFetcherValueError(self):
"""
If the sequence fetcher throws a C{ValueError}, the feature list
must have length zero and should not be marked as being offline.
"""
def fetcher(title, db):
raise ValueError()
featureList = FeatureList('title', 'database', set(),
sequenceFetcher=fetcher)
self.assertEqual(0, len(featureList))
self.assertEqual(False, featureList.offline)
def testNotSubfeature(self):
"""
If the sequence fetcher returns a record with a feature that is
not a subfeature, it must not be marked as a subfeature.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature = SeqFeature(type='site', qualifiers={'a': ['b']},
location=location)
return SeqRecord(None, features=[feature])
featureList = FeatureList('title', 'database', set(['site']),
sequenceFetcher=fetcher)
self.assertFalse(featureList[0].subfeature)
def testNoQualifiersLength(self):
"""
If the sequence fetcher returns a record with two features but
neither of them has any qualifiers, the L{FeatureList} instance
must still include both features.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature = SeqFeature(type='site', location=location)
return SeqRecord(None, features=[feature, feature])
featureList = FeatureList('title', 'database', set(['site']),
sequenceFetcher=fetcher)
self.assertEqual(2, len(featureList))
def testWantedTypeLength(self):
"""
If the sequence fetcher returns a record with two features but
only one of them has a wanted type ('site'), the L{FeatureList}
instance must have length one.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature1 = SeqFeature(type='region', location=location)
feature2 = SeqFeature(type='site', qualifiers={'a': ['b']},
location=location)
return SeqRecord(None, features=[feature1, feature2])
featureList = FeatureList('title', 'database', set(['site']),
sequenceFetcher=fetcher)
self.assertEqual(1, len(featureList))
def testColors(self):
"""
If the sequence fetcher returns a record with 3 features, each
must be assigned a correct color.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
feature = SeqFeature(type='site', qualifiers={'a': ['b']},
location=location)
return SeqRecord(None, features=[feature] * 3)
featureList = FeatureList('title', 'database', set(['site']),
sequenceFetcher=fetcher)
colormap = plt.cm.coolwarm
colors = [colormap(i) for i in np.linspace(0.0, 0.99, 3)]
for i in range(3):
self.assertEqual(colors[i], featureList[i].color)
def testSubfeatures(self):
"""
If the sequence fetcher returns a record with a feature that
has a subfeature, the L{FeatureList} instance must have length two
and the second feature in the list must be a subfeature.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
subfeature = SeqFeature(type='site',
qualifiers={'a': ['b']},
location=location)
feature = SeqFeature(type='site',
qualifiers={'a': ['b']},
sub_features=[subfeature],
location=location)
return SeqRecord(None, features=[feature])
featureList = FeatureList('title',
'database',
set(['site']),
sequenceFetcher=fetcher)
self.assertEqual(2, len(featureList))
self.assertTrue(featureList[1].subfeature)
def testSubfeaturesWithoutParentFeature(self):
"""
If the sequence fetcher returns a record with a feature that
has a subfeature, and the subfeature is wanted but the parent feature
is not, the L{FeatureList} instance must have length one
and the feature in the list must be a subfeature.
"""
def fetcher(title, db='database'):
location = FeatureLocation(100, 200)
subfeature = SeqFeature(type='region',
qualifiers={'a': ['b']},
location=location)
feature = SeqFeature(type='site',
qualifiers={'a': ['b']},
sub_features=[subfeature],
location=location)
return SeqRecord(None, features=[feature])
featureList = FeatureList('title',
'database',
set(['region']),
sequenceFetcher=fetcher)
self.assertEqual(1, len(featureList))
self.assertTrue(featureList[0].subfeature)
