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

source code

  object --+    
           |    
_Motif.Motif --+
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              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)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
_numoccurrences(self, number) source code
 
get_instance_by_name(self, name) source code
 
add_instance_from_values(self, name='default', pvalue=1, sequence='ATA', start=0, strand='+') source code
 
_evalue(self, evalue) source code

Inherited from _Motif.Motif: __getitem__, __len__, __str__, add_instance, anticonsensus, consensus, dist_dpq, dist_dpq_at, dist_pearson, dist_pearson_at, dist_product, dist_product_at, exp_score, format, ic, log_odds, make_counts_from_instances, make_instances_from_counts, max_score, min_score, pwm, reverse_complement, scanPWM, score_hit, search_instances, search_pwm, set_mask, weblogo

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)