def __call__(self, threshold, alphabet_len=None, use_loose=True):
"""Returns a MotifResults object containing a list of significant Motifs
- When a Module is found that is less than the threshold, a new
Motif object is created and added to the list of significant
motifs.
"""
#Create new MotifResults object
k_word_results = MotifResults()
k_word_results.Modules = []
k_word_results.Motifs = []
#Add alignment to MotifResults
k_word_results.Alignment = self.Alignment
#Give each module a unique ID
module_id = 0
#For each module
for i, module in enumerate(self.Modules):
if use_loose:
p_curr = self.getPValueLoose(module, alphabet_len)
else:
p_curr = self.getPValueStrict(module, alphabet_len)
#If the P value is less than or equal to the threshold
if p_curr <= threshold:
#Add the P value to the current module
module.Pvalue = p_curr
module.ID = module_id
module_id += 1
#Append the module to the k_word_results Modules list
k_word_results.Modules.append(module)
#Create a Motif from the module and append to Motifs list
k_word_results.Motifs.append(Motif(module))
return k_word_results
def __call__(self, threshold, alphabet_len=None, use_loose=True):
"""Returns a MotifResults object containing a list of significant Motifs
- When a Module is found that is less than the threshold, a new
Motif object is created and added to the list of significant
motifs.
"""
# Create new MotifResults object
k_word_results = MotifResults()
k_word_results.Modules = []
k_word_results.Motifs = []
# Add alignment to MotifResults
k_word_results.Alignment = self.Alignment
# Give each module a unique ID
module_id = 0
# For each module
for i, module in enumerate(self.Modules):
if use_loose:
p_curr = self.getPValueLoose(module, alphabet_len)
else:
p_curr = self.getPValueStrict(module, alphabet_len)
# If the P value is less than or equal to the threshold
if p_curr <= threshold:
# Add the P value to the current module
module.Pvalue = p_curr
module.ID = module_id
module_id += 1
# Append the module to the k_word_results Modules list
k_word_results.Modules.append(module)
# Create a Motif from the module and append to Motifs list
k_word_results.Motifs.append(Motif(module))
return k_word_results
