def test_row_degeneracy(self):
"""row_degeneracy: should work with different cutoff values and arrays
"""
a = array([[.1, .3, .4, .2],[.5, .3, 0, .2],[.8, 0, .1, .1]])
self.assertEqual(row_degeneracy(a,cutoff=.75),[3,2,1])
self.assertEqual(row_degeneracy(a,cutoff=.95),[4,3,3])
#one-dimensional array
self.assertRaises(ValueError, row_degeneracy,\
array([.25,.25,.25,.25]))
#if cutoff value is not found, results are clipped to the
#number of columns in the array
self.assertEqual(row_degeneracy(a,cutoff=2), [4,4,4])
#same behavior on empty array
self.assertEqual(row_degeneracy(array([[]])),[])
def rowDegeneracy(self, cutoff=0.5):
"""Returns how many chars are needed to cover the cutoff value.
cutoff: value that should be covered in each row
For example:
pos 0: [.1,.2,.3,.4] char order=TCAG.
If cutoff=0.75 -> degeneracy = 3 (degenearate char for CAG)
If cutoff=0.25 -> degeneracy = 1 (G alone covers this cutoff)
If cutoff=0.5 -> degeneracy = 2 (degenerate char for AG)
If the cutoff value is not reached in the row, the returned value
will be clipped to the length of the character order (=the number
of columns in the Profile).
"""
try:
return row_degeneracy(self.Data, cutoff)
except ValueError:
raise ProfileError, "Profile has to be two dimensional to calculate rowDegeneracy"
def rowDegeneracy(self, cutoff=0.5):
"""Returns how many chars are needed to cover the cutoff value.
cutoff: value that should be covered in each row
For example:
pos 0: [.1,.2,.3,.4] char order=TCAG.
If cutoff=0.75 -> degeneracy = 3 (degenearate char for CAG)
If cutoff=0.25 -> degeneracy = 1 (G alone covers this cutoff)
If cutoff=0.5 -> degeneracy = 2 (degenerate char for AG)
If the cutoff value is not reached in the row, the returned value
will be clipped to the length of the character order (=the number
of columns in the Profile).
"""
try:
return row_degeneracy(self.Data,cutoff)
except ValueError:
raise ProfileError("Profile has to be two dimensional to calculate rowDegeneracy")