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 GibbsParser(lines, truncate_len=None, strict=True):
"""Returns a MotifResults object given a Gibbs Sampler results file.
- only works with results from command line version of Gibbs Sampler
"""
try:
#Get sequence and motif blocks
sequence_block, motif_block = get_sequence_and_motif_blocks(lines)
except Exception as e:
if strict:
raise e
else:
return None
#Create MotifResults object
gibbs_motif_results = MotifResults()
#Get sequence map
sequence_map = get_sequence_map(sequence_block)
#Get motif blocks
motif_blocks = get_motif_blocks(motif_block)
#Get modules
for module in motif_blocks:
if module[1] == 'No Motifs Detected':
print("No Modules detcted!!", module[0])
continue
for cur_smod in build_module_objects(module,
sequence_map,
truncate_len=truncate_len):
gibbs_motif_results.Modules.append(cur_smod)
module_ids_to_int(gibbs_motif_results.Modules)
for ct, module in enumerate(gibbs_motif_results.Modules):
gibbs_motif_results.Motifs.append(Motif(module))
gibbs_motif_results.Alphabet = module.Alphabet
return gibbs_motif_results
def test_init(self):
"""Init should properly initialize Motif object."""
module = Module({
('a',3): ModuleInstance('guc', Location('a',3,5)),
('b',3): ModuleInstance('guc', Location('b',3,5)),
('c',8): ModuleInstance('guc', Location('c',8,10)),
})
m = Motif(module)
self.assertEqual(m.Modules,[module])
self.assertEqual(m.Info,None)
def MemeParser(lines, allowed_ids=[]):
"""Returns a MotifResults object given a MEME results file.
"""
warnings = []
#Create MotifResults object
meme_motif_results = MotifResults()
#Get main block and alphabet
main_block, alphabet = getDataBlock(lines)
#Add alphabet to MotifResults object
meme_motif_results.MolType = alphabet
#Get command line summary block and module blocks
command_block, module_blocks = getCommandModuleBlocks(main_block)
if command_block:
#Extract command line data and put in dict
parameters_list = extractCommandLineData(command_block)
#Add parameters dict to MotifResults object parameters
meme_motif_results.Parameters = parameters_list
#make sure modules were found
if len(module_blocks) > 0:
#Get Summary of motifs block
summary_block = getSummaryBlock(module_blocks[-1])
#Extract summary data and get summary_dict
summary_dict = extractSummaryData(summary_block)
seq_names = list(summary_dict['CombinedP'].keys())
if allowed_ids:
remap_dict, warning = make_remap_dict(seq_names, allowed_ids)
if warning:
warnings.append(warning)
sd = {}
for k, v in list(summary_dict['CombinedP'].items()):
sd[remap_dict[k]] = v
summary_dict['CombinedP'] = sd
else:
remap_dict = dict(list(zip(seq_names, seq_names)))
#Add summary dict to MotifResults object
meme_motif_results.Results = summary_dict
#Add warnings to MotifResults object
meme_motif_results.Results['Warnings'] = warnings
#Get blocks for each module
module_blocks = getModuleDataBlocks(module_blocks)
#Extract modules and put in MotifResults.Modules list
for module in module_blocks:
meme_motif_results.Modules.append(extractModuleData(module,\
alphabet,remap_dict))
for module in meme_motif_results.Modules:
meme_motif_results.Motifs.append(Motif(module))
return meme_motif_results
def test_init(self):
"""Init should properly initialize MotifResults object."""
module = Module({
('a',3): ModuleInstance('guc', Location('a',3,5)),
('b',3): ModuleInstance('guc', Location('b',3,5)),
('c',8): ModuleInstance('guc', Location('c',8,10)),
})
motif = Motif([module])
results = {'key1':'value1','key2':'value2'}
parameters = {'parameter1':1,'parameter2':2}
mr = MotifResults([module],[motif],results,parameters)
self.assertEqual(mr.Modules,[module])
self.assertEqual(mr.Motifs,[motif])
self.assertEqual(mr.Results,results)
self.assertEqual(mr.parameter1,1)
self.assertEqual(mr.parameter2,2)
sequence_map = get_sequence_map(sequence_block)
#Get motif blocks
motif_blocks = get_motif_blocks(motif_block)
#Get modules
for module in motif_blocks:
if module[1] == 'No Motifs Detected':
print "No Modules detcted!!", module[0]
continue
for cur_smod in build_module_objects(module,
sequence_map,
truncate_len=truncate_len):
gibbs_motif_results.Modules.append(cur_smod)
module_ids_to_int(gibbs_motif_results.Modules)
for ct, module in enumerate(gibbs_motif_results.Modules):
gibbs_motif_results.Motifs.append(Motif(module))
gibbs_motif_results.Alphabet = module.Alphabet
return gibbs_motif_results
if __name__ == "__main__":
from sys import argv, exit
print "Running..."
if len(argv) != 2:
print "Usage: gibbs.py <gibbs out file>"
exit(1)
mr = GibbsParser(open(argv[1]), 24)
print mr
for module in mr.Modules:
print module.ID