def toCartesian(self, round_error=1e-14):
"""Returns new MagePoint with UC,UG,UA coordinates from A,C,G(,U).
round_error -- float, accepted rounding error
x=u+c, y=u+g, z=u+a
This will only work for coordinates in a simplex, where all of them
(inlcuding the implicit one) add up to one.
"""
# all values have to be between 0 and 1
a = fix_rounding_error(self.X)
c = fix_rounding_error(self.Y)
g = fix_rounding_error(self.Z)
# u = fix_rounding_error(1-a-c-g)
if is_essentially(1, a + c + g, round_error=round_error):
u = 0.0
else:
u = fix_rounding_error(1 - a - c - g)
for coord in [a, c, g, u]:
if not 0 <= coord <= 1:
raise ValueError, "%s is not in unit simplex (between 0 and 1)" % (coord)
cart_x, cart_y, cart_z = u + c, u + g, u + a
result = deepcopy(self)
result.Coordinates = [cart_x, cart_y, cart_z]
return result
def toCartesian(self, round_error=1e-14):
"""Returns new MagePoint with UC,UG,UA coordinates from A,C,G(,U).
round_error -- float, accepted rounding error
x=u+c, y=u+g, z=u+a
This will only work for coordinates in a simplex, where all of them
(inlcuding the implicit one) add up to one.
"""
# all values have to be between 0 and 1
a = fix_rounding_error(self.X)
c = fix_rounding_error(self.Y)
g = fix_rounding_error(self.Z)
#u = fix_rounding_error(1-a-c-g)
if is_essentially(1, a+c+g, round_error=round_error):
u = 0.0
else:
u = fix_rounding_error(1-a-c-g)
for coord in [a,c,g,u]:
if not 0 <= coord <= 1:
raise ValueError,\
"%s is not in unit simplex (between 0 and 1)"%(coord)
cart_x, cart_y, cart_z = u+c, u+g, u+a
result = deepcopy(self)
result.Coordinates = [cart_x, cart_y, cart_z]
return result
def stdtri(k, p):
"""Returns inverse of Student's t distribution. k = df."""
p = fix_rounding_error(p)
# handle easy cases
if k <= 0 or p < 0.0 or p > 1.0:
raise ZeroDivisionError, "k must be >= 1, p between 1 and 0."
rk = k
#handle intermediate values
if p > 0.25 and p < 0.75:
if p == 0.5:
return 0.0
z = 1.0 - 2.0 * p
z = incbi(0.5, 0.5 * rk, abs(z))
t = sqrt(rk * z / (1.0 - z))
if p < 0.5:
t = -t
return t
#handle extreme values
rflg = -1
if p >= 0.5:
p = 1.0 - p
rflg = 1
z = incbi(0.5 * rk, 0.5, 2.0 * p)
if MAXNUM * z < rk:
return rflg * MAXNUM
t = sqrt(rk / z - rk)
return rflg * t
def stdtri(k, p):
"""Returns inverse of Student's t distribution. k = df."""
p = fix_rounding_error(p)
# handle easy cases
if k <= 0 or p < 0.0 or p > 1.0:
raise ZeroDivisionError, "k must be >= 1, p between 1 and 0."
rk = k
#handle intermediate values
if p > 0.25 and p < 0.75:
if p == 0.5:
return 0.0
z = 1.0 - 2.0 * p;
z = incbi(0.5, 0.5*rk, abs(z))
t = sqrt(rk*z/(1.0-z))
if p < 0.5:
t = -t
return t
#handle extreme values
rflg = -1
if p >= 0.5:
p = 1.0 - p;
rflg = 1
z = incbi(0.5*rk, 0.5, 2.0*p)
if MAXNUM * z < rk:
return rflg * MAXNUM
t = sqrt(rk/z - rk)
return rflg * t
def pdtri(k, p):
"""Inverse of Poisson distribution.
Finds Poission mean such that integral from 0 to k is p.
"""
p = fix_rounding_error(p)
if k < 0 or p < 0.0 or p >= 1.0:
raise ZeroDivisionError, "k must be >=0, p between 1 and 0."
v = k + 1
return igami(v, p)
def pdtri(k, p):
"""Inverse of Poisson distribution.
Finds Poission mean such that integral from 0 to k is p.
"""
p = fix_rounding_error(p)
if k < 0 or p < 0.0 or p >= 1.0:
raise ZeroDivisionError, "k must be >=0, p between 1 and 0."
v = k+1;
return igami(v, p)
def gdtri(a, b, y):
"""Returns Gamma such that y is the probability in the integral.
WARNING: if 1-y == 1, gives incorrect result. The scipy implementation
gets around this by using cdflib, which is in Fortran. Until someone
gets around to translating that, only use this function for values of
p greater than 1e-15 or so!
"""
y = fix_rounding_error(y)
if y < 0.0 or y > 1.0 or a <= 0.0 or b < 0.0:
raise ZeroDivisionError, "a and b must be non-negative, y from 0 to 1."
return igami(b, 1.0-y) / a
def gdtri(a, b, y):
"""Returns Gamma such that y is the probability in the integral.
WARNING: if 1-y == 1, gives incorrect result. The scipy implementation
gets around this by using cdflib, which is in Fortran. Until someone
gets around to translating that, only use this function for values of
p greater than 1e-15 or so!
"""
y = fix_rounding_error(y)
if y < 0.0 or y > 1.0 or a <= 0.0 or b < 0.0:
raise ZeroDivisionError, "a and b must be non-negative, y from 0 to 1."
return igami(b, 1.0 - y) / a
def angle(v1,v2):
"""
calculates the angle between two vectors.
v1 and v2 are numpy.array objects.
returns a float containing the angle in radians.
"""
length_product = norm(v1)*norm(v2)
if length_product == 0:
raise AngleGeometryError(\
"Cannot calculate angle for vectors with length zero")
cosine = scalar(v1,v2)/length_product
angle = acos(fix_rounding_error(cosine))
return angle
def angle(v1,v2):
"""
calculates the angle between two vectors.
v1 and v2 are numpy.array objects.
returns a float containing the angle in radians.
"""
length_product = norm(v1)*norm(v2)
if length_product == 0:
raise AngleGeometryError(\
"Cannot calculate angle for vectors with length zero")
cosine = scalar(v1,v2)/length_product
angle = acos(fix_rounding_error(cosine))
return angle
def fromCartesian(self):
"""Returns new MagePoint with A,C,G(,U) coordinates from UC,UG,UA.
From UC,UG,UA to A,C,G(,U).
This will only work when the original coordinates come from a simplex,
where U+C+A+G=1
"""
# x=U+C, y=U+G, z=U+A, U+C+A+G=1
# U=(1-x-y-z)/-2
x, y, z = self.X, self.Y, self.Z
u = fix_rounding_error((1 - x - y - z) / -2)
a, c, g = map(fix_rounding_error, [z - u, x - u, y - u])
result = deepcopy(self)
result.Coordinates = [a, c, g]
return result
def fromCartesian(self):
"""Returns new MagePoint with A,C,G(,U) coordinates from UC,UG,UA.
From UC,UG,UA to A,C,G(,U).
This will only work when the original coordinates come from a simplex,
where U+C+A+G=1
"""
# x=U+C, y=U+G, z=U+A, U+C+A+G=1
# U=(1-x-y-z)/-2
x,y,z = self.X, self.Y, self.Z
u = fix_rounding_error((1-x-y-z)/-2)
a, c, g = map(fix_rounding_error,[z-u, x-u, y-u])
result = deepcopy(self)
result.Coordinates = [a, c, g]
return result
def fromCartesian(cls, *coords):
"""Returns new BaseUsage with A,C,G,U coordinates from UC,UG,UA.
From UC,UG,UA to A,C,G(,U).
This will only work when the original coordinates come from a simplex,
where U+C+A+G=1
"""
result = cls()
x,y,z = coords
u = fix_rounding_error((1-x-y-z)/-2)
a, c, g = z-u, x-u, y-u
result['A'] = a
result['C'] = c
result['G'] = g
result['U'] = u
return result
def fdtri(a, b, y):
"""Returns inverse of F distribution."""
y = fix_rounding_error(y)
if( a < 1.0 or b < 1.0 or y <= 0.0 or y > 1.0):
raise ZeroDivisionError, "y must be between 0 and 1; a and b >= 1"
y = 1.0-y
# Compute probability for x = 0.5
w = incbet(0.5*b, 0.5*a, 0.5)
# If that is greater than y, then the solution w < .5.
# Otherwise, solve at 1-y to remove cancellation in (b - b*w).
if w > y or y < 0.001:
w = incbi(0.5*b, 0.5*a, y)
x = (b - b*w)/(a*w)
else:
w = incbi(0.5*a, 0.5*b, 1.0-y)
x = b*w/(a*(1.0-w))
return x
def fdtri(a, b, y):
"""Returns inverse of F distribution."""
y = fix_rounding_error(y)
if (a < 1.0 or b < 1.0 or y <= 0.0 or y > 1.0):
raise ZeroDivisionError, "y must be between 0 and 1; a and b >= 1"
y = 1.0 - y
# Compute probability for x = 0.5
w = incbet(0.5 * b, 0.5 * a, 0.5)
# If that is greater than y, then the solution w < .5.
# Otherwise, solve at 1-y to remove cancellation in (b - b*w).
if w > y or y < 0.001:
w = incbi(0.5 * b, 0.5 * a, y)
x = (b - b * w) / (a * w)
else:
w = incbi(0.5 * a, 0.5 * b, 1.0 - y)
x = b * w / (a * (1.0 - w))
return x
def chi_high(x, df):
"""Returns right-hand tail of chi-square distribution (x to infinity).
df, the degrees of freedom, ranges from 1 to infinity (assume integers).
Typically, df is (r-1)*(c-1) for a r by c table.
Result ranges from 0 to 1.
See Cephes docs for details.
"""
x = fix_rounding_error(x)
if x < 0:
raise ValueError, "chi_high: x must be >= 0 (got %s)." % x
if df < 1:
raise ValueError, "chi_high: df must be >= 1 (got %s)." % df
return igamc(df / 2, x / 2)
def fromCartesian(cls, *coords):
"""Returns new BaseUsage with A,C,G,U coordinates from UC,UG,UA.
From UC,UG,UA to A,C,G(,U).
This will only work when the original coordinates come from a simplex,
where U+C+A+G=1
"""
result = cls()
x, y, z = coords
u = fix_rounding_error((1 - x - y - z) / -2)
a, c, g = z - u, x - u, y - u
result['A'] = a
result['C'] = c
result['G'] = g
result['U'] = u
return result
def chi_high(x, df):
"""Returns right-hand tail of chi-square distribution (x to infinity).
df, the degrees of freedom, ranges from 1 to infinity (assume integers).
Typically, df is (r-1)*(c-1) for a r by c table.
Result ranges from 0 to 1.
See Cephes docs for details.
"""
x = fix_rounding_error(x)
if x < 0:
raise ValueError, "chi_high: x must be >= 0 (got %s)." % x
if df < 1:
raise ValueError, "chi_high: df must be >= 1 (got %s)." % df
return igamc(df/2, x/2)
def bdtr(k, n, p):
"""Binomial distribution, 0 through k.
Uses formula bdtr(k, n, p) = betai(n-k, k+1, 1-p)
See Cephes docs for details.
"""
p = fix_rounding_error(p)
if (p < 0) or (p > 1):
raise ValueError, "Binomial p must be between 0 and 1."
if (k < 0) or (n < k):
raise ValueError, "Binomial k must be between 0 and n."
if k == n:
return 1
dn = n - k
if k == 0:
return pow(1 - p, dn)
else:
return betai(dn, k + 1, 1 - p)
def bdtr(k, n, p):
"""Binomial distribution, 0 through k.
Uses formula bdtr(k, n, p) = betai(n-k, k+1, 1-p)
See Cephes docs for details.
"""
p = fix_rounding_error(p)
if (p < 0) or (p > 1):
raise ValueError, "Binomial p must be between 0 and 1."
if (k < 0) or (n < k):
raise ValueError, "Binomial k must be between 0 and n."
if k == n:
return 1
dn = n - k
if k == 0:
return pow(1-p, dn)
else:
return betai(dn, k+1, 1-p)
def bdtrc(k, n, p):
"""Complement of binomial distribution, k+1 through n.
Uses formula bdtrc(k, n, p) = betai(k+1, n-k, p)
See Cephes docs for details.
"""
p = fix_rounding_error(p)
if (p < 0) or (p > 1):
raise ValueError, "Binomial p must be between 0 and 1."
if (k < 0) or (n < k):
raise ValueError, "Binomial k must be between 0 and n."
if k == n:
return 0
dn = n - k
if k == 0:
if p < .01:
dk = -expm1(dn * log1p(-p))
else:
dk = 1 - pow(1.0 - p, dn)
else:
dk = k + 1
dk = betai(dk, dn, p)
return dk
def bdtri(k, n, y):
"""Inverse of binomial distribution.
Finds binomial p such that sum of terms 0-k reaches cum probability y.
"""
y = fix_rounding_error(y)
if y < 0.0 or y > 1.0:
raise ZeroDivisionError, "y must be between 1 and 0."
if k < 0 or n <= k:
raise ZeroDivisionError, "k must be between 0 and n"
dn = n - k
if k == 0:
if y > 0.8:
p = -expm1(log1p(y-1.0) / dn)
else:
p = 1.0 - y**(1.0/dn)
else:
dk = k + 1;
p = incbet(dn, dk, 0.5)
if p > 0.5:
p = incbi(dk, dn, 1.0-y)
else:
p = 1.0 - incbi(dn, dk, y)
return p
def bdtri(k, n, y):
"""Inverse of binomial distribution.
Finds binomial p such that sum of terms 0-k reaches cum probability y.
"""
y = fix_rounding_error(y)
if y < 0.0 or y > 1.0:
raise ZeroDivisionError, "y must be between 1 and 0."
if k < 0 or n <= k:
raise ZeroDivisionError, "k must be between 0 and n"
dn = n - k
if k == 0:
if y > 0.8:
p = -expm1(log1p(y - 1.0) / dn)
else:
p = 1.0 - y**(1.0 / dn)
else:
dk = k + 1
p = incbet(dn, dk, 0.5)
if p > 0.5:
p = incbi(dk, dn, 1.0 - y)
else:
p = 1.0 - incbi(dn, dk, y)
return p
def bdtrc(k, n, p):
"""Complement of binomial distribution, k+1 through n.
Uses formula bdtrc(k, n, p) = betai(k+1, n-k, p)
See Cephes docs for details.
"""
p = fix_rounding_error(p)
if (p < 0) or (p > 1):
raise ValueError, "Binomial p must be between 0 and 1."
if (k < 0) or (n < k):
raise ValueError, "Binomial k must be between 0 and n."
if k == n:
return 0
dn = n - k
if k == 0:
if p < .01:
dk = -expm1(dn * log1p(-p))
else:
dk = 1 - pow(1.0-p, dn)
else:
dk = k + 1
dk = betai(dk, dn, p)
return dk
def chdtri(df, y):
"""Returns inverse of chi-squared distribution."""
y = fix_rounding_error(y)
if(y < 0.0 or y > 1.0 or df < 1.0):
raise ZeroDivisionError, "y must be between 0 and 1; df >= 1"
return 2 * igami(0.5*df, y)
def chdtri(df, y):
"""Returns inverse of chi-squared distribution."""
y = fix_rounding_error(y)
if (y < 0.0 or y > 1.0 or df < 1.0):
raise ZeroDivisionError, "y must be between 0 and 1; df >= 1"
return 2 * igami(0.5 * df, y)
