/usr/lib/python2.7/dist-packages/cogent/evolve/substitution_calculation.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 | #!/usr/bin/env python
import numpy
import warnings
from cogent.recalculation.definition import PositiveParamDefn, RatioParamDefn, \
CalculationDefn, MonotonicDefn, ProductDefn, ConstDefn, PartitionDefn, \
NonParamDefn, CallDefn, SelectForDimension, \
GammaDefn, WeightedPartitionDefn, CalcDefn
from cogent.maths.matrix_exponentiation import PadeExponentiator, \
FastExponentiator, CheckedExponentiator, LinAlgError
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
# Custom subclasses of Defn (see cogent.recalulation) for use by substitution models.
class AlignmentAdaptDefn(CalculationDefn):
name = 'leaf_likelihoods'
def calc(self, model, alignment):
return model.convertAlignment(alignment)
class LengthDefn(PositiveParamDefn):
name = 'length'
valid_dimensions = ('edge',)
independent_by_default = True
upper = 10.0
class RateDefn(RatioParamDefn):
name = 'rate'
valid_dimensions = ('bin', 'locus')
independent_by_default = True
lower = 1e-3
upper = 1e+3
class SubstitutionParameterDefn(RatioParamDefn):
valid_dimensions = ('edge', 'bin', 'locus')
independent_by_default = False
class ExpDefn(CalculationDefn):
name = 'exp'
def calc(self, expm):
(allow_eigen, check_eigen, allow_pade) = {
'eigen': (True, False, False),
'checked': (True, True, False),
'pade': (False, False, True),
'either': (True, True, True),
}[str(expm)]
if not allow_eigen:
return PadeExponentiator
eigen = CheckedExponentiator if check_eigen else FastExponentiator
if not allow_pade:
return eigen
else:
def _both(Q, eigen=eigen):
try:
return eigen(Q)
except (ArithmeticError, LinAlgError), detail:
if not _both.given_expm_warning:
warnings.warn("using slow exponentiator because '%s'"
% str(detail))
_both.given_expm_warning = True
return PadeExponentiator(Q)
_both.given_expm_warning = False
return _both
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