Package Bio :: Package MEME :: Module Motif :: Class MEMEMotif
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Class MEMEMotif

source code

Motif --+
        |
       MEMEMotif

A subclass of Motif used in parsing MEME (and MAST) output.

This sublcass defines functions and data specific to MEME motifs. This includes the evalue for a motif and the PSSM of the motif.

Methods: add_instance_from_values (name = 'default', pvalue = 1, sequence = 'ATA', start = 0, strand = +): create a new instance of the motif with the specified values. add_to_pssm (position): add a new position to the pssm. The position should be a list of nucleotide/amino acid frequencies add_to_logodds (position): add a new position to the log odds matrix. The position should be a tuple of log odds values for the nucleotide/amino acid at that position. compare_motifs (other_motif): returns the maximum correlation between this motif and other_motif

Instance Methods [hide private]
 
__init__(self) source code
 
add_instance_from_values(self, name='default', pvalue=1, sequence='ATA', start=0, strand='+') source code
 
_evalue(self, evalue) source code
 
add_to_pssm(self, thisposition) source code
 
add_to_logodds(self, thisposition) source code
 
compare_motifs(self, motif) source code

Inherited from Motif: add_instance, get_instance_by_name, make_consensus, make_pssm

Inherited from Motif (private): _alphabet, _consensus, _length, _name, _numoccurrences

Method Details [hide private]

__init__(self)
(Constructor)

source code 
Overrides: Motif.__init__