def to_logodds_scoring_matrix( self, background=None, correction=DEFAULT_CORRECTION ):
        """
        Create a standard logodds scoring matrix.
        """
        alphabet_size = len( self.alphabet )
        if background is None:
            background = ones( alphabet_size, float32 ) / alphabet_size
        # Row totals as a one column array
        totals = numpy.sum( self.values, 1 )[:,newaxis]
        values = log2( maximum( self.values, correction ) ) \
               - log2( totals ) \
               - log2( maximum( background, correction ) )
        return ScoringMatrix.create_from_other( self, values.astype( float32 ) )
def to_logodds_scoring_matrix ( self , background = None , correction = DEFAULT_CORRECTION ) : alphabet_size = len ( self . alphabet ) if background is None : background = ones ( alphabet_size , float32 ) / alphabet_size totals = numpy . sum ( self . values , 1 ) [ : , newaxis ] values = log2 ( maximum ( self . values , correction ) ) - log2 ( totals ) - log2 ( maximum ( background , correction ) ) return ScoringMatrix . create_from_other ( self , values . astype ( float32 ) )
Create a standard logodds scoring matrix.