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
| Method Summary |
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__init__(self)
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add_instance_from_values(self,
name,
pvalue,
sequence,
start,
strand)
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add_to_logodds(self,
thisposition)
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add_to_pssm(self,
thisposition)
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compare_motifs(self,
motif)
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_evalue(self,
evalue)
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| Inherited from Motif |
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add_instance(self,
instance) |
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get_instance_by_name(self,
name) |
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make_consensus(self,
minimum_frequency) |
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make_pssm(self) |
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_alphabet(self,
alphabet) |
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_consensus(self,
consensus) |
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_length(self,
length) |
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_name(self,
name) |
| |
_numoccurrences(self,
number) |