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Package Bio :: Package AlignAce :: Module Motif :: Class Motif |
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object
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Motif
Method Summary | |
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__init__(self)
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string representation of motif | |
adds new instance to the motif | |
returns the PWM computed for the set of instances | |
reads the motif from the stream | |
give the pwm score for a given position | |
a generator function, returning found positions of instances of the motif in a given sequence | |
a generator function, returning found hits in a given sequence with the pwm score higher than the threshold | |
sets the mask for the motif | |
return the similarity score for the given motif against self. | |
writes the motif to the stream | |
_check_alphabet(self,
alphabet)
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_check_length(self,
len)
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Inherited from object | |
x.__delattr__('name') <==> del x.name | |
x.__getattribute__('name') <==> x.name | |
x.__hash__() <==> hash(x) | |
T.__new__(S, ...) -> a new object with type S, a subtype of T | |
helper for pickle | |
helper for pickle | |
x.__repr__() <==> repr(x) | |
x.__setattr__('name', value) <==> x.name = value |
Method Details |
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__str__(self)
string representation of motif
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add_instance(self, instance)adds new instance to the motif |
pwm(self)returns the PWM computed for the set of instances |
read(self, stream)reads the motif from the stream the self.alphabet variable must be set before |
score_hit(self, sequence, position, normalized=1, masked=0)give the pwm score for a given position |
search_instances(self, sequence)a generator function, returning found positions of instances of the motif in a given sequence |
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 |
set_mask(self, mask)sets the mask for the motif The mask should be a string containing asterisks in the position of significant columns and spaces in other columns |
sim(self, motif, masked=0)return the similarity score for the given motif against self. We use the Pearson's correlation of the respective probabilities. If the motifs have different length or mask raise the ValueError. |
write(self, stream)writes the motif to the stream |
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