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Bio.Motif.Parsers.MEME.MEMEMotif Class Reference
Inheritance diagram for Bio.Motif.Parsers.MEME.MEMEMotif:
Collaboration diagram for Bio.Motif.Parsers.MEME.MEMEMotif:

List of all members.

Public Member Functions

def __init__
def add_instance_from_values
def get_instance_by_name

Public Attributes


Private Member Functions

def _evalue
def _numoccurrences

Detailed Description

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.

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

Definition at line 58 of file MEME.py.

The documentation for this class was generated from the following file:

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