def testTwoPathsTwoBubbles(self):
db = {}
clusters = []
exons1 = [self.a1, self.b1, self.d1, self.f1, self.g1]
exons2 = [self.a2, self.c2, self.d2, self.e2, self.g2]
comp.addExon(db, clusters, exons1)
comp.addExon(db, clusters, exons2)
path = []
allPaths = []
comp.walkDown(self.a1.coord, path, allPaths, self.a1.cluster)
self.assertEqual(len(allPaths), 4)
expectedAllPaths = [[self.b1.coord,
self.d1.coord,
self.f1.coord,
self.g1.coord],
[self.b1.coord,
self.d1.coord,
self.e2.coord,
self.g1.coord],
[self.c2.coord,
self.d1.coord,
self.f1.coord,
self.g1.coord],
[self.c2.coord,
self.d1.coord,
self.e2.coord,
self.g1.coord]]
self.assertListEqual(expectedAllPaths, allPaths)
def testTwoPaths(self):
db = {}
clusters = []
exons1 = [self.a1, self.b1, self.c1, self.d1]
exons2 = [self.a2, self.b2, self.c2, self.e2]
comp.addExon(db, clusters, exons1)
comp.addExon(db, clusters, exons2)
path = []
allPath = []
comp.walkDown(self.c2.coord, path, allPath, self.c2.cluster)
self.assertEqual(len(allPath), 2)
path = []
allPath = []
comp.walkDown(self.a2.coord, path, allPath, self.a2.cluster)
self.assertEqual(len(allPath), 2)
self.assertEqual(
allPath[0],
[str(self.b1), str(self.c1),
str(self.d1)])
self.assertEqual(
allPath[1],
[str(self.b2), str(self.c2),
str(self.e2)])
def testSingleExonPath(self):
db = {}
clusters = []
exons1 = [self.a1]
comp.addExon(db, clusters, exons1)
path = []
allPath = []
comp.walkDown(self.a1.coord, path, allPath, self.a1.cluster)
self.assertEqual(len(allPath), 1)
self.assertEqual(allPath, [[]])
def testSingleExonPath(self):
db = {}
clusters = []
exons1 = [self.a1]
comp.addExon(db, clusters, exons1)
path = []
allPath = []
comp.walkDown(self.a1.coord, path, allPath, self.a1.cluster)
self.assertEqual(len(allPath), 1)
self.assertEqual(allPath, [[]])
def testSinglePath(self):
db = {}
clusters = []
exons1 = [self.a1, self.b1, self.c1, self.d1, self.e1]
comp.addExon(db, clusters, exons1)
path = []
allPath = []
comp.walkDown(self.a1.coord, path, allPath, self.a1.cluster)
self.assertEqual(len(allPath), 1)
self.assertEqual(allPath, [[str(self.b1), str(self.c1),
str(self.d1), str(self.e1)]])
def testSinglePath(self):
db = {}
clusters = []
exons1 = [self.a1, self.b1, self.c1, self.d1, self.e1]
comp.addExon(db, clusters, exons1)
path = []
allPath = []
comp.walkDown(self.a1.coord, path, allPath, self.a1.cluster)
self.assertEqual(len(allPath), 1)
self.assertEqual(
allPath, [[str(self.b1),
str(self.c1),
str(self.d1),
str(self.e1)]])
def testTwoPaths(self):
db = {}
clusters = []
exons1 = [self.a1, self.b1, self.c1, self.d1]
exons2 = [self.a2, self.b2, self.c2, self.e2]
comp.addExon(db, clusters, exons1)
comp.addExon(db, clusters, exons2)
path = []
allPath = []
comp.walkDown(self.c2.coord, path, allPath, self.c2.cluster)
self.assertEqual(len(allPath), 2)
path = []
allPath = []
comp.walkDown(self.a2.coord, path, allPath, self.a2.cluster)
self.assertEqual(len(allPath), 2)
self.assertEqual(allPath[0], [str(self.b1), str(self.c1), str(self.d1)])
self.assertEqual(allPath[1], [str(self.b2), str(self.c2), str(self.e2)])
def testTwoPathsTwoBubbles(self):
db = {}
clusters = []
exons1 = [self.a1, self.b1, self.d1, self.f1, self.g1]
exons2 = [self.a2, self.c2, self.d2, self.e2, self.g2]
comp.addExon(db, clusters, exons1)
comp.addExon(db, clusters, exons2)
path = []
allPaths = []
comp.walkDown(self.a1.coord, path, allPaths, self.a1.cluster)
self.assertEqual(len(allPaths), 4)
expectedAllPaths = [
[self.b1.coord, self.d1.coord, self.f1.coord, self.g1.coord],
[self.b1.coord, self.d1.coord, self.e2.coord, self.g1.coord],
[self.c2.coord, self.d1.coord, self.f1.coord, self.g1.coord],
[self.c2.coord, self.d1.coord, self.e2.coord, self.g1.coord]
]
self.assertListEqual(expectedAllPaths, allPaths)