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src/c/o/cogent-1.5.3/cogent/motif/k_word.py   cogent(Download)
#!/usr/bin/env python
"""MotifFinder that searches for over-represented k-words in an alignment."""
 
from __future__ import division
from cogent.motif.util import Motif, Module, ModuleFinder, ModuleConsolidator, \
class KWordModuleConsolidatorNucleotide(ModuleConsolidator):
    """Consolidates module instances obtained from an alignment into modules.
 
        - Must be initialized with an instance of KWordModuleFinder
    """
class KWordModuleConsolidatorProtein(ModuleConsolidator):
    """Consolidates module instances obtained from an alignment into modules.
 
        - Must be initialized with an instance of KWordModuleFinder
    """
class KWordModuleFilterProtein(ModuleConsolidator):
    """Filters list of Modules by number of Modules and seqs where Module is in.
 
        - This is a strict ModuleConsolidator.  Does not allow mismatches, but
        rather consolidates based on a minimum allowed modules and minimum

src/p/y/pycogent-HEAD/cogent/motif/k_word.py   pycogent(Download)
#!/usr/bin/env python
"""MotifFinder that searches for over-represented k-words in an alignment."""
 
from __future__ import division
from cogent.motif.util import Motif, Module, ModuleFinder, ModuleConsolidator, \
class KWordModuleConsolidatorNucleotide(ModuleConsolidator):
    """Consolidates module instances obtained from an alignment into modules.
 
        - Must be initialized with an instance of KWordModuleFinder
    """
class KWordModuleConsolidatorProtein(ModuleConsolidator):
    """Consolidates module instances obtained from an alignment into modules.
 
        - Must be initialized with an instance of KWordModuleFinder
    """
class KWordModuleFilterProtein(ModuleConsolidator):
    """Filters list of Modules by number of Modules and seqs where Module is in.
 
        - This is a strict ModuleConsolidator.  Does not allow mismatches, but
        rather consolidates based on a minimum allowed modules and minimum