A class representing sequence motifs.
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__init__(self)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature |
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add_instance(self,
instance)
adds new instance to the motif |
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pwm(self)
returns the PWM computed for the set of instances |
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search_instances(self,
sequence)
a generator function, returning found positions of instances of the
motif in a given sequence |
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score_hit(self,
sequence,
position,
normalized=1,
masked=0)
give the pwm score for a given position |
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search_pwm(self,
sequence,
threshold=0.0,
normalized=1,
masked=1)
a generator function, returning found hits in a given sequence with
the pwm score higher than the threshold |
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sim(self,
motif,
masked=0)
return the similarity score for the given motif against self. |
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write(self,
stream)
writes the motif to the stream |
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to_fasta(self)
FASTA representation of motif |
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weblogo(self,
fname,
format=' PNG ' ,
**kwds)
uses the Berkeley weblogo service to download and save a weblogo of
itself |
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Inherited from object :
__delattr__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__
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