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
