def testFindOneClusterEnd(self):
"""
The find method must find a cluster at the end of a sequence.
"""
read = AARead('id', 'AAAAAAAAKKAH')
finder = ClusterAlphaHelix()
result = list(finder.find(read))
self.assertEqual([Landmark('ClusterAlphaHelix', 'CAH', 8, 4, '1131')],
result)
def testFindOneClusterBeginning(self):
"""
The find method must find one cluster at the beginning of a sequence.
"""
read = AARead('id', 'KKAHFFFFFFFFF')
finder = ClusterAlphaHelix()
result = list(finder.find(read))
self.assertEqual([Landmark('ClusterAlphaHelix', 'CAH', 0, 4, '1131')],
result)
def testFindWithoutCluster(self):
"""
The find method must return an empty generator when no alpha helix
cluster is present.
"""
read = AARead('id', 'FFFFFFFFFFFFFFFFFFFFFFFFFFF')
finder = ClusterAlphaHelix()
result = list(finder.find(read))
self.assertEqual([], result)
def testFindTwoIdenticalAAClustersNonIdenticalAAAdjacent(self):
"""
The find method must find two identical clusters with a different AA
sequence.
"""
read = AARead('id', 'KKAHRKMH')
finder = ClusterAlphaHelix()
result = list(finder.find(read))
self.assertEqual([
Landmark('ClusterAlphaHelix', 'CAH', 0, 4, '1131'),
Landmark('ClusterAlphaHelix', 'CAH', 4, 4, '1131')
], result)
def testFindTwoIdenticalClustersNonIdenticalAANotAdjacent(self):
"""
The find method must find repeating identical clusters that come from
a different AA sequence.
"""
read = AARead('id', 'KKAHAAAAAAAARKMH')
finder = ClusterAlphaHelix()
result = list(finder.find(read))
self.assertEqual([
Landmark('ClusterAlphaHelix', 'CAH', 0, 4, '1131'),
Landmark('ClusterAlphaHelix', 'CAH', 12, 4, '1131')
], result)
def testThreeDifferentClustersTwoOccurences(self):
"""
The find method must find three different clusters with two occurences
each.
"""
read = AARead('id', 'KKAHGHLVKVIGKKAHGHLVKVIG')
finder = ClusterAlphaHelix()
result = list(finder.find(read))
self.assertEqual([
Landmark('ClusterAlphaHelix', 'CAH', 0, 4, '1131'),
Landmark('ClusterAlphaHelix', 'CAH', 4, 4, '2144'),
Landmark('ClusterAlphaHelix', 'CAH', 8, 4, '1442'),
Landmark('ClusterAlphaHelix', 'CAH', 12, 4, '1131'),
Landmark('ClusterAlphaHelix', 'CAH', 16, 4, '2144'),
Landmark('ClusterAlphaHelix', 'CAH', 20, 4, '1442')
], result)