/usr/share/pyshared/cogent/evolve/bootstrap.py is in python-cogent 1.5.3-2.
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 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 | #!/usr/bin/env python
"""
Provides services for parametric bootstrapping. These include
the ability to estimate probabilities or estimate confidence intervals.
The estimation of probabilities is done by the EstimateProbability class.
Functions that provide ParameterController objects for the 'null' and
'alternative' cases are provided to the constructor. Numerous aspects of the
bootstrapping can be controlled such as the choice of numerical optimiser, and
the number of samples from which to estimate the probability. This class
can be run in serial or in parallel (at the level of each random sample).
An observed Likelihood Ratio (LR) statistic is estimated using the provided
'observed' data. Random data sets are simulated under the null model and the
LR estimated from these. The probability of the observed LR is taken as the
number of sample LR's that were >= to the observed.
Confidence interval estimation can be done using the EstimateConfidenceIntervals
class. Multiple statistics associated with an analysis can be evaluated
simultaneously. Similar setup, and parallelisation options as provided by
the EstimateProbability class.
"""
from __future__ import with_statement, division
from cogent.util import parallel
from cogent.util import progress_display as UI
import random
__author__ = "Gavin Huttley, Andrew Butterfield and Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Gavin Huttley","Andrew Butterfield", "Matthew Wakefield",
"Edward Lang", "Peter Maxwell"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
class ParametricBootstrapCore(object):
"""Core parametric bootstrap services."""
def __init__(self):
"""Constructor for core parametric bootstrap services class."""
self._numreplicates = 10
self.seed = None
self.results = []
def setNumReplicates(self, num):
self._numreplicates = num
def setSeed(self, seed):
self.seed = seed
@UI.display_wrap
def run(self, ui, **opt_args):
# Sets self.observed and self.results (a list _numreplicates long) to
# whatever is returned from self.simplify([LF result from each PC]).
# self.simplify() is used as the entire LF result might not be picklable
# for MPI. Subclass must provide self.alignment and
# self.parameter_controllers
if 'random_series' not in opt_args and not opt_args.get('local', None):
opt_args['random_series'] = random.Random()
null_pc = self.parameter_controllers[0]
pcs = len(self.parameter_controllers)
if pcs == 1:
model_label = ['']
elif pcs == 2:
model_label = ['null', 'alt ']
else:
model_label = ['null'] + ['alt%s'%i for i in range(1,pcs)]
@UI.display_wrap
def each_model(alignment, ui):
def one_model(pc):
pc.setAlignment(alignment)
return pc.optimise(return_calculator=True, **opt_args)
# This is not done in parallel because we depend on the side-
# effect of changing the parameter_controller current values
memos = ui.eager_map(one_model, self.parameter_controllers,
labels=model_label, pure=False)
concise_result = self.simplify(*self.parameter_controllers)
return (memos, concise_result)
#optimisations = pcs * (self._numreplicates + 1)
init_work = pcs / (self._numreplicates + pcs)
ui.display('Original data', 0.0, init_work)
(starting_points, self.observed) = each_model(self.alignment)
ui.display('Randomness', init_work, 0.0)
alignment_random_state = random.Random(self.seed).getstate()
if self.seed is None:
comm = parallel.getCommunicator()
alignment_random_state = comm.bcast(alignment_random_state, 0)
def one_replicate(i):
for (pc, start_point) in zip(self.parameter_controllers, starting_points):
# may have fewer CPUs per replicate than for original
pc.setupParallelContext()
# using a calculator as a memo object to reset the params
pc.updateFromCalculator(start_point)
aln_rnd = random.Random(0)
aln_rnd.setstate(alignment_random_state)
aln_rnd.jumpahead(i*10**9)
simalign = null_pc.simulateAlignment(random_series=aln_rnd)
(dummy, result) = each_model(simalign)
return result
ui.display('Bootstrap', init_work)
self.results = ui.eager_map(
one_replicate, range(self._numreplicates), noun='replicate',
start=init_work)
class EstimateProbability(ParametricBootstrapCore):
# 2 parameter controllers, LR
def __init__(self, null_parameter_controller, alt_parameter_controller, alignment):
ParametricBootstrapCore.__init__(self)
self.alignment = alignment
self.null_parameter_controller = null_parameter_controller
self.alt_parameter_controller = alt_parameter_controller
self.parameter_controllers = [self.null_parameter_controller, self.alt_parameter_controller]
def simplify(self, null_result, alt_result):
return (null_result.getLogLikelihood(), alt_result.getLogLikelihood())
def getObservedlnL(self):
return self.observed
def getSamplelnL(self):
return self.results
def getSampleLRList(self):
LR = [2 * (alt_lnL - null_lnL) for (null_lnL, alt_lnL) in self.results]
LR.sort()
LR.reverse()
return LR
def getObservedLR(self):
return 2 * (self.observed[1] - self.observed[0])
def getEstimatedProb(self):
"""Return the estimated probability.
Calculated as the number of sample LR's >= observed LR
divided by the number of replicates.
"""
observed_LR = self.getObservedLR()
sample_LRs = self.getSampleLRList()
for (count, value) in enumerate(sample_LRs):
if value <= observed_LR:
return float(count) / len(sample_LRs)
return 1.0
class EstimateConfidenceIntervals(ParametricBootstrapCore):
"""Estimate confidence interval(s) for one or many statistics
by parametric bootstrapping."""
def __init__(self, parameter_controller, func_calcstats, alignment):
# func_calcstats takes a param dict and returns the statistic of interest
ParametricBootstrapCore.__init__(self)
self.alignment = alignment
self.parameter_controller = parameter_controller
self.parameter_controllers = [parameter_controller]
self.func_calcstats = func_calcstats
def simplify(self, result):
return (result.getLogLikelihood(), self.func_calcstats(result))
def getObservedStats(self):
return self.observed[1]
def getSampleStats(self):
return [s for (lnL, s) in self.results]
def getSamplelnL(self):
return [lnL for (lnL, s) in self.results]
def getObservedlnL(self):
return self.observed[0]
|