def test_known_vals(self):
"""Composition should return precalculated elements for known cases"""
self.assertEqual(len(Composition(5,1,"ACGU")), 969)
self.assertEqual(len(Composition(5,0,"ACGU")), 1771)
as_list = list(Composition(5,1,"ACGU"))
self.assertEqual(as_list[0], Freqs('A'*17+'CGU'))
self.assertEqual(as_list[-1], Freqs('U'*17+'ACG'))
def setUp(self):
"""Define a few standard compositions."""
self.bases_10pct = Composition(10, 0, "ACGU")
self.bases_5pct = Composition(5, 1, "ACGU")
self.bases_extra = Composition(10, 0, "CYGEJ")
self.small = Composition(20, 0, "xy")
self.unique = Composition(20, 1, "z")
def test_updating(self):
"""Composition updates should reset frequencies correctly."""
exp_list = list(Composition(5, 1, "GCAUN"))
self.bases_10pct.Spacing = 5
self.bases_10pct.Alphabet = "GCAUN"
self.bases_10pct.MinOccupancy = 1
self.assertEqual(list(self.bases_10pct), exp_list)
def setUp(self):
"""Define a few standard compositions."""
self.bases_10pct = Composition(10, 0, "ACGU")