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
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 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 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 = 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 summary_dict['CombinedP'].items():
sd[remap_dict[k]]=v
summary_dict['CombinedP']=sd
else:
remap_dict = dict(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)
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 setUp(self):
"""SetUp for MotifFormatter class tests."""
self.sequences = [
'accucua',
'caucguu',
'accucua',
'cgacucg',
'cgaucag',
'cuguacc',
'cgcauca',
]
self.locations = [
Location('seq0',1,3),
Location('seq1',2,3),
Location('seq1',1,5),
Location('seq1',5,3),
Location('seq2',3,54),
Location('seq2',54,2),
Location('seq3',4,0),
]
self.Pvalues = [
.1,
.002,
.0000000003,
.6,
.0094,
.6,
.00201,
]
self.Evalues = [
.006,
.02,
.9,
.0200000001,
.09,
.0000003,
.900001,
]
self.modules_no_e = []
for i in xrange(7):
self.modules_no_e.append(ModuleInstance(self.sequences[i],
self.locations[i],
self.Pvalues[i]))
self.module_with_template = Module(
{
(self.modules_no_e[0].Location.SeqId,
self.modules_no_e[0].Location.Start):self.modules_no_e[0],
(self.modules_no_e[1].Location.SeqId,
self.modules_no_e[1].Location.Start):self.modules_no_e[1],
(self.modules_no_e[2].Location.SeqId,
self.modules_no_e[2].Location.Start):self.modules_no_e[2],
(self.modules_no_e[3].Location.SeqId,
self.modules_no_e[3].Location.Start):self.modules_no_e[3],
(self.modules_no_e[4].Location.SeqId,
self.modules_no_e[4].Location.Start):self.modules_no_e[4],
(self.modules_no_e[5].Location.SeqId,
self.modules_no_e[5].Location.Start):self.modules_no_e[5],
(self.modules_no_e[6].Location.SeqId,
self.modules_no_e[6].Location.Start):self.modules_no_e[6],
},
Template = 'accgucg', ID='1'
)
self.modules_with_ids =\
[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)),
},ID='1'),
Module({
('a',7): ModuleInstance('cca', Location('a',7,9)),
('b',7): ModuleInstance('cca', Location('b',7,9)),
('c',11): ModuleInstance('cca',Location('c',11,13)),
},ID='2'),
Module({
('a',10): ModuleInstance('gca',Location('a',10,12)),
('b',10): ModuleInstance('gca',Location('b',10,12)),
('c',14): ModuleInstance('gca',Location('c',14,12)),
},ID='3'),
Module({
('a',13): ModuleInstance('ggg',Location('a',13,15)),
('b',13): ModuleInstance('ggg',Location('b',13,15)),
('c',18): ModuleInstance('ggg',Location('c',18,20)),
},ID='4'),
]
self.motifs_with_ids = map(Motif,self.modules_with_ids)
self.motif_results = MotifResults(Modules=self.modules_with_ids,\
Motifs=self.motifs_with_ids)
self.color_map = {'1':"""background-color: #0000FF; ; font-family: 'Courier New', Courier""",
'2':"""background-color: #FFFF00; ; font-family: 'Courier New', Courier""",
'3':"""background-color: #00FFFF; ; font-family: 'Courier New', Courier""",
'4':"""background-color: #FF00FF; ; font-family: 'Courier New', Courier""",
}
self.color_map_rgb = {
'color_1':(0.0,0.0,1.0),
'color_2':(1.0,1.0,0.0),
'color_3':(0.0,1.0,1.0),
'color_4':(1.0,0.0,1.0),
}
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, 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)
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, 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):