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src/c/o/cogent-1.5.3/cogent/core/moltype.py   cogent(Download)
__status__ = "Production"
 
from cogent.core.alphabet import CharAlphabet, Enumeration, Alphabet, \
    AlphabetError, _make_complement_array
from cogent.util.misc import FunctionWrapper, add_lowercase, iterable, if_
                self.Alphabet = CharAlphabet(motifset, MolType=self)
            else:
                self.Alphabet = Alphabet(motifset, MolType=self)
        #set the other properties
        self.Degenerates = Ambiguities and Ambiguities.copy() or {}
class _CodonAlphabet(Alphabet):
    """Codon alphabets are DNA TupleAlphabets with a genetic code attribute and some codon-specific methods"""
 
    def _with(self, motifs):
        a = Alphabet._with(self, motifs)

src/p/y/pycogent-HEAD/cogent/core/moltype.py   pycogent(Download)
__status__ = "Production"
 
from cogent.core.alphabet import CharAlphabet, Enumeration, Alphabet, \
    AlphabetError, _make_complement_array
from cogent.util.misc import FunctionWrapper, add_lowercase, iterable, if_
                self.Alphabet = CharAlphabet(motifset, MolType=self)
            else:
                self.Alphabet = Alphabet(motifset, MolType=self)
        #set the other properties
        self.Degenerates = Ambiguities and Ambiguities.copy() or {}
class _CodonAlphabet(Alphabet):
    """Codon alphabets are DNA TupleAlphabets with a genetic code attribute and some codon-specific methods"""
 
    def _with(self, motifs):
        a = Alphabet._with(self, motifs)

src/c/o/cogent-1.5.3/cogent/evolve/coevolution.py   cogent(Download)
from cogent.core.moltype import IUPAC_gap, IUPAC_missing
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.maths.stats.special import ROUND_ERROR

src/p/y/pycogent-HEAD/cogent/evolve/coevolution.py   pycogent(Download)
from cogent.core.moltype import IUPAC_gap, IUPAC_missing
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.maths.stats.special import ROUND_ERROR

src/c/o/cogent-1.5.3/tests/test_seqsim/test_usage.py   cogent(Download)
from cogent.core.moltype import RNA
from cogent.core.usage import RnaBases, DnaBases, RnaPairs, DnaPairs
from cogent.core.alphabet import Alphabet
from cogent.core.sequence import ModelRnaSequence as RnaSequence, \
    ModelRnaCodonSequence
    from test_stats.test_util import StaticFreqsTestsI
 
    my_alpha = Alphabet('abcde')
    class myUsage(Usage):
        Alphabet = my_alpha
    def setUp(self):
        """Defines some standard test items."""
        self.ab = Alphabet('ab')
 
        class abUsage(Usage):
    def setUp(self):
        """Define standard alphabet and matrices for tests."""
        self.ab = Alphabet('ab')
        self.ab_pairs = self.ab*self.ab
        self.empty = PairMatrix([0,0,0,0], self.ab_pairs)
 
        #should work even if SubAlphabets not the same
        a = Alphabet('ab')
        x = Alphabet('xyz')
        j = a * x

src/p/y/pycogent-HEAD/tests/test_seqsim/test_usage.py   pycogent(Download)
from cogent.core.moltype import RNA
from cogent.core.usage import RnaBases, DnaBases, RnaPairs, DnaPairs
from cogent.core.alphabet import Alphabet
from cogent.core.sequence import ModelRnaSequence as RnaSequence, \
    ModelRnaCodonSequence
    from test_stats.test_util import StaticFreqsTestsI
 
    my_alpha = Alphabet('abcde')
    class myUsage(Usage):
        Alphabet = my_alpha
    def setUp(self):
        """Defines some standard test items."""
        self.ab = Alphabet('ab')
 
        class abUsage(Usage):
    def setUp(self):
        """Define standard alphabet and matrices for tests."""
        self.ab = Alphabet('ab')
        self.ab_pairs = self.ab*self.ab
        self.empty = PairMatrix([0,0,0,0], self.ab_pairs)
 
        #should work even if SubAlphabets not the same
        a = Alphabet('ab')
        x = Alphabet('xyz')
        j = a * x

src/c/o/cogent-1.5.3/tests/test_evolve/test_coevolution.py   cogent(Download)
from cogent.maths.stats.util import Freqs
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.core.alignment import DenseAlignment
            rate_matrix=array(count_matrix_3),\
            motif_probs=aa_freqs_3,\
            alphabet=Alphabet(aa_order_3),recode_gaps=True,do_scaling=True,\
            name="",optimise_motif_probs=False)
        wprobs = array([aa_freqs_3[aa] for aa in aa_order_3])

src/p/y/pycogent-HEAD/tests/test_evolve/test_coevolution.py   pycogent(Download)
from cogent.maths.stats.util import Freqs
from cogent.core.profile import Profile
from cogent.core.alphabet import CharAlphabet, Alphabet
from cogent.maths.stats.distribution import binomial_exact
from cogent.core.alignment import DenseAlignment
            rate_matrix=array(count_matrix_3),\
            motif_probs=aa_freqs_3,\
            alphabet=Alphabet(aa_order_3),recode_gaps=True,do_scaling=True,\
            name="",optimise_motif_probs=False)
        wprobs = array([aa_freqs_3[aa] for aa in aa_order_3])

src/p/y/pycogent-HEAD/tests/test_util/test_recode_alignment.py   pycogent(Download)
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel
from cogent.core.alphabet import Alphabet 
from cogent.app.gctmpca import gctmpca_aa_order,\
 default_gctmpca_aa_sub_matrix

src/c/o/cogent-1.5.3/tests/test_util/test_recode_alignment.py   cogent(Download)
from cogent.evolve.models import DSO78_matrix, DSO78_freqs
from cogent.evolve.substitution_model import SubstitutionModel
from cogent.core.alphabet import Alphabet 
from cogent.app.gctmpca import gctmpca_aa_order,\
 default_gctmpca_aa_sub_matrix