A class representing sequence motifs.
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__getitem__(self,
index)
Returns the probability distribution over symbols at a given
position, padding with background. |
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__init__(self,
alphabet=IUPACUnambiguousDNA())
x.__init__(...) initializes x; see help(type(x)) for signature |
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_from_horiz_matrix(self,
stream,
letters=None,
make_instances=False)
reads a horizontal count matrix from stream and fill in the counts. |
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_from_vert_matrix(self,
stream,
letters=None,
make_instances=False)
reads a vertical count matrix from stream and fill in the counts. |
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_read(self,
stream)
Reads the motif from the stream (in AlignAce format). |
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_to_fasta(self)
FASTA representation of motif |
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_to_horizontal_matrix(self,
letters=None,
normalized=True)
Return string representation of the motif as a matrix. |
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_to_jaspar_pfm(self)
Returns the pfm representation of the motif |
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_to_transfac(self)
Write the representation of a motif in TRANSFAC format |
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_to_vertical_matrix(self,
letters=None)
Return string representation of the motif as a matrix. |
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_write(self,
stream)
writes the motif to the stream |
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add_instance(self,
instance)
adds new instance to the motif |
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anticonsensus(self)
returns the least probable pattern to be generated from this motif. |
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consensus(self)
Returns the consensus sequence of a motif. |
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dist_pearson(self,
motif,
masked=0)
return the similarity score based on pearson correlation for the
given motif against self. |
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dist_product(self,
other)
A similarity measure taking into account a product probability of
generating overlaping instances of two motifs |
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exp_score(self,
st_dev=False)
Computes expected score of motif's instance and its standard
deviation |
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format(self,
format)
Returns a string representation of the Motif in a given format |
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ic(self)
Method returning the information content of a motif. |
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log_odds(self,
laplace=True)
returns the logg odds matrix computed for the set of instances |
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make_counts_from_instances(self)
Creates the count matrix for a motif with instances. |
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pwm(self,
laplace=True)
returns the PWM computed for the set of instances |
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reverse_complement(self)
Gives the reverse complement of the motif |
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score_hit(self,
sequence,
position,
normalized=0,
masked=0)
give the pwm score for a given position |
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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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search_pwm(self,
sequence,
normalized=0,
masked=0,
threshold=0.0,
both=True)
a generator function, returning found hits in a given sequence with
the pwm score higher than the threshold |
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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__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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