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src/r/n/rnaseqlib-HEAD/rnaseqlib/motif/dinuc_freq.py   rnaseqlib(Download)
 
import cogent
from cogent.core.usage import DinucUsage
 
import rnaseqlib
        self.len = len(seq)
        # Calculate dinuc. frequencies
        self.du = DinucUsage(seq, Overlapping=overlapping)
        if normalize:
            self.du.normalize()

src/c/o/cogent-1.5.3/tests/test_core/test_usage.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import FunctionWrapper
from cogent.core.usage import InfoFreqs, AminoAcidUsage, BaseUsage, CodonUsage,\
    PositionalBaseUsage, UnsafeBaseUsage, EqualBases, DinucUsage
from cogent.core.genetic_code import GeneticCodes, GeneticCode
    def test_distance(self):
        """Dinuc distance should calculate Euclidean dist. correctly"""
        s1 ='AA'+'GG'*10
        s2 = 'AA'*5 + 'GG'*7
        d1 = DinucUsage(s1, Overlapping=False)
        d2 = DinucUsage(s2, Overlapping=False)

src/p/y/pycogent-HEAD/tests/test_core/test_usage.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import FunctionWrapper
from cogent.core.usage import InfoFreqs, AminoAcidUsage, BaseUsage, CodonUsage,\
    PositionalBaseUsage, UnsafeBaseUsage, EqualBases, DinucUsage
from cogent.core.genetic_code import GeneticCodes, GeneticCode
    def test_distance(self):
        """Dinuc distance should calculate Euclidean dist. correctly"""
        s1 ='AA'+'GG'*10
        s2 = 'AA'*5 + 'GG'*7
        d1 = DinucUsage(s1, Overlapping=False)
        d2 = DinucUsage(s2, Overlapping=False)

src/r/n/rnaseqlib-HEAD/rnaseqlib/motif/seq_counter.py   rnaseqlib(Download)
 
import cogent
from cogent.core.usage import DinucUsage
 
import rnaseqlib