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)
def __init__(self, arguments=None):
# Initialize the parser object
parser = argparse.ArgumentParser()
# ---------------- Mandatory arguments ------------------ #
# Add 'alphabetType' as an argument
parser.add_argument("alphabetType",
help="Each genotype in the input file must be a string " +
"of letters from the alphabet selected here.",
choices=BitManipFactory.getMoleculeTypes())
# Add 'includeIndels' as an argument
parser.add_argument("includeIndels",
help="Should be set to 'True' if mutations that shift " +
"the entire genotype sequence by one letter should " +
"also be considered. Only single point mutations are " +
"considered when this parameter is set to 'False'.",
choices=["True", "true", "False", "false"])
# Add 'inFilePath' as an argument
parser.add_argument("inFilePath",
help="Complete path to the input file, relative to the " +
"current directory.")
# Add 'tau' as an argument
parser.add_argument("tau",
help="Minimum score threshold: all genotypes in the input " +
"file with 'score' values below 'Tau' will be ignored." +
"Tau must be a number.",
type=float)
# Add 'outPath' as an argument
parser.add_argument("outPath",
help="Path to the directory where output files should be " +
"generated. The directory will be created if it does " +
"not already exist.")
# ---------------- Optional arguments ------------------ #
# Add 'use_reverse_complements' as an argument
parser.add_argument("-rc", "--use_reverse_complements", dest="use_reverse_complements", action="store_const",
const=True,
help="When specified, reverse complements are considered during creation " +
"and analysis of genotype networks for alphabet type DNA. This option is " +
"not valid for other alphabet types.")
# Add 'num_processes' as an argument
parser.add_argument("-np", "--num_processes", dest="num_procs", action="store",
type=int, default="4",
help="No. of processes to be used in parallel processing")
# Add 'verbose' as an argument
parser.add_argument("-v", "--verbose", dest="verbose", action="store_const",
const=True,
help="Processing steps are printed to the screen during " +
"program execution.")
# Keep an object level copy of the arguments dict
if arguments:
# Parse the string of arguments received
self.args = parser.parse_args(arguments)
else:
# Parse sys.argv
self.args = parser.parse_args()