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src/c/o/cogent-1.5.3/cogent/seqsim/markov.py

**cogent**(Download)

from operator import mul from random import choice, shuffle, randrange from cogent.maths.stats.util import UnsafeFreqs as Freqs from cogent.util.array import cartesian_product from cogent.maths.stats.test import G_fit

curr = all_freqs.get(word, None) if curr is None: curr = Freqs({next:1}) all_freqs[word] = curr else:

can just feed the whole thing into a single Freqs. """ freqs = Freqs('') for line in self.Text: freqs += line

result = dict.fromkeys(map(''.join, cartesian_product([a]*k))) for k in result: result[k] = Freqs(dict(zip(a, random_f(len(a))))) return result

src/p/y/pycogent-HEAD/cogent/seqsim/markov.py

**pycogent**(Download)

from operator import mul from random import choice, shuffle, randrange from cogent.maths.stats.util import UnsafeFreqs as Freqs from cogent.util.array import cartesian_product from cogent.maths.stats.test import G_fit

curr = all_freqs.get(word, None) if curr is None: curr = Freqs({next:1}) all_freqs[word] = curr else:

can just feed the whole thing into a single Freqs. """ freqs = Freqs('') for line in self.Text: freqs += line

result = dict.fromkeys(map(''.join, cartesian_product([a]*k))) for k in result: result[k] = Freqs(dict(zip(a, random_f(len(a))))) return result

src/c/o/cogent-1.5.3/cogent/core/usage.py

**cogent**(Download)

#!/usr/bin/env python """Classes for dealing with base, codon, and amino acid usage. """ from __future__ import division from cogent.maths.stats.util import Freqs, Numbers, UnsafeFreqs

class UnsafeBaseUsage(BaseUsageI, UnsafeFreqs): """Stores frequencies of the four bases. Does not do any validation. This class avoids overriding most built-ins, so is much faster than BaseFreqs (although it is often less convenient).

class UnsafeCodonUsage(CodonUsageI, UnsafeFreqs): """Stores frequencies of the four bases. Must access as RNA. This class avoids overriding most built-ins, so is much faster than CodonFreqs (although it is often less convenient).

src/p/y/pycogent-HEAD/cogent/core/usage.py

**pycogent**(Download)

#!/usr/bin/env python """Classes for dealing with base, codon, and amino acid usage. """ from __future__ import division from cogent.maths.stats.util import Freqs, Numbers, UnsafeFreqs

class UnsafeBaseUsage(BaseUsageI, UnsafeFreqs): """Stores frequencies of the four bases. Does not do any validation. This class avoids overriding most built-ins, so is much faster than BaseFreqs (although it is often less convenient).

class UnsafeCodonUsage(CodonUsageI, UnsafeFreqs): """Stores frequencies of the four bases. Must access as RNA. This class avoids overriding most built-ins, so is much faster than CodonFreqs (although it is often less convenient).

src/p/y/pycogent-HEAD/tests/test_maths/test_stats/test_util.py

**pycogent**(Download)

import numpy from cogent.util.unit_test import TestCase, main from cogent.maths.stats.util import SummaryStatistics, SummaryStatisticsError,\ Numbers, UnsafeNumbers, Freqs, UnsafeFreqs, NumberFreqs, \ UnsafeNumberFreqs

src/c/o/cogent-1.5.3/tests/test_maths/test_stats/test_util.py

**cogent**(Download)

import numpy from cogent.util.unit_test import TestCase, main from cogent.maths.stats.util import SummaryStatistics, SummaryStatisticsError,\ Numbers, UnsafeNumbers, Freqs, UnsafeFreqs, NumberFreqs, \ UnsafeNumberFreqs