def _create_gn(seqScrDict, args, seqLength, resultsQueue, repertoire):
# Get a reference to the bit manipulator
bitManip = BitManipFactory.getBitSeqManip(args.moleculeType,
seqLength,
args.useIndels,
args.use_reverse_complements)
# Get the sequences for the given repertoire
sequences = seqScrDict.keys()
# Get the list of scores for the given repertoire
scores = [seqScrDict[sequence] for sequence in sequences]
# Create a network builder object
netBuilder = NetworkBuilder(bitManip)
# Create the genotype network
network = netBuilder.createGenoNet(repertoire, sequences, scores)
# Get the number of components in the network
numComponents = len(netBuilder.getComponents(network))
# If there are more than one components,
if numComponents > 1:
# Get the giant component
giant = netBuilder.getGiantComponent(network)
# Set 'name' attribute for giant
giant["name"] = repertoire + "_dominant"
else:
# The network and giant component are the same
giant = network
# Create a tuple in which to put the results
netTuple = (repertoire, (network, giant))
# Add the created network objects to the shared queue
resultsQueue.put(netTuple)
# Close the queue for this process
resultsQueue.close()
def _bit_manipulator(self):
return BitManipFactory.getBitSeqManip(self.cmdArgs.moleculeType,
self.seqLength,
self.cmdArgs.useIndels,
self.cmdArgs.use_reverse_complements)