def build_module_objects(motif_block, sequence_map, truncate_len=None):
"""Returns module object given a motif_block and sequence_map.
- motif_block is list of lines resulting from calling get_motif_blocks
- sequence_map is the mapping between Gibbs sequence numbering and
sequence id from fasta file.
"""
#Get motif id
motif_id = motif_block[0].strip().split()[-1]
#Get motif_list
motif_list = get_motif_sequences(motif_block)
#Get motif p-value
motif_p = get_motif_p_value(motif_block)
#Guess alphabet from motif sequences
alphabet = guess_alphabet(motif_list)
#Create Module object(s)
all_modules = {}
# DISABLED FOR NOW
#module_keys = set([x[4] for x in motif_list])
module_keys = ["1"]
for k in module_keys:
cur_mod = Module({}, Alphabet=alphabet)
cur_mod.Pvalue = motif_p
cur_mod.ID = motif_id + k
all_modules[k] = cur_mod
for motif in motif_list:
seq_id = str(sequence_map[motif[0]])
if truncate_len:
seq_id = seq_id[:truncate_len]
start = motif[1]
seq = motif[2]
sig = motif[3]
#motif_num = motif[4]
motif_num = "1"
#Create Location object
location = Location(seq_id, start, start + len(seq))
#Create ModuleInstance
mod_instance = ModuleInstance(seq,location,sig)
cur_key = (seq_id,start)
all_modules[motif_num][(seq_id,start)]=mod_instance
for gmod in all_modules.values():
yield gmod
def extractModuleData(module_data, alphabet):
"""Creates Module object given module_data list.
- Only works on 1 module at a time: only pass in data from one module.
"""
# Create Module object
meme_module = Module({}, Alphabet=alphabet)
# Only keep first 3 elements of the list
module_data = module_data[:3]
# Get Module general information: module_data[0]
# Only need to keep first line
general_dict = getModuleGeneralInfo(module_data[0][0])
# Get Multilevel Consensus Sequence
meme_module.ConsensusSequence = getConsensusSequence(module_data[1])
# Pull out desired values from dict
module_length = int(general_dict["width"])
meme_module.Llr = int(general_dict["llr"])
meme_module.Evalue = float(general_dict["E-value"])
meme_module.ID = general_dict["MOTIF"]
# Get ModuleInstances: module_data[2]
instance_data = module_data[2][4:-2]
for i in xrange(len(instance_data)):
instance_data[i] = instance_data[i].split()
# Create a ModuleInstance object and add it to Module for each instance
for instance in instance_data:
seqId = instance[0]
start = int(instance[1]) - 1
Pvalue = float(instance[2])
sequence = instance[4]
# Create Location object for ModuleInstance
location = Location(seqId, start, start + module_length)
# Create ModuleInstance
mod_instance = ModuleInstance(sequence, location, Pvalue)
# Add ModuleInstance to Module
meme_module[(seqId, start)] = mod_instance
return meme_module
