def main():
parser = OptionParser(
description="Merges the split histograms of two or more HRG consensus dendrograms. Creates a new consensus dendrogram from the merged histograms. Saves the new consensus dendrogram to a graph markup language (GML) file.",
prog='hrg-merge-histograms.py',
usage='%prog [options] GRAPH_EDGELIST_FILE PICKLED_HISTOGRAM ... PICKLED_HISTOGRAM OUTPUT_FILE')
parser.add_option('-f', '--force', action='store', type=int, default=10000,
help='Allow overwriting of existing GML dendrogram files')
(options, args) = parser.parse_args()
if len(args) < 4:
parser.print_help()
return 1
graph_edgelist = args[0]
G = nx.read_edgelist(graph_edgelist, nodetype=int)
filename = os.path.basename(graph_edgelist)
G.name = os.path.splitext(filename)[0]
args.remove(graph_edgelist)
outfile=args.pop()
if os.path.exists(outfile) and not options.force:
raise Exception("Output file " + outfile +
" exists. Won't overwrite without --force option.")
n = 0
histograms = []
for histfile in args:
f = open(histfile, 'rb')
histogram = pickle.load(f)
if not isinstance(histogram, collections.Mapping):
raise Exception('Object in ' + histfile +
' is not a dictionary: ' + str(type(histogram)))
if n == 0:
n = histogram['num_samples']
if histogram['num_samples'] != n:
raise Exception('inconsistent number of samples, '
'expected ' + str(n) + ', actual ' +
histogram['num_samples'])
del histogram['num_samples']
histograms.append(histogram)
nodes = G.nodes()
nodes.sort()
builder = ConsensusDendrogramBuilder()
C = builder.build(nodes, histograms, n)
# Save the consensus dendrogram to a GML file.
nx.write_gml(C, outfile)
print("Saved merged consensus dendrogram to " + outfile + ".")
return 0
def main():
parser = OptionParser(
description="Merges the split histograms of two or more hrg consensus dendrograms. Creates a new consensus dendrogram from the merged histograms. Saves the new consensus dendrogram to a graph markup language (GML) file.",
prog='hrg-merge-histograms.py',
usage='%prog [options] GRAPH_EDGELIST_FILE PICKLED_HISTOGRAM ... PICKLED_HISTOGRAM OUTPUT_FILE')
parser.add_option('-f', '--force', action='store', type=int, default=10000,
help='Allow overwriting of existing GML dendrogram files')
(options, args) = parser.parse_args()
if len(args) < 4:
parser.print_help()
return 1
graph_edgelist = args[0]
G = nx.read_edgelist(graph_edgelist, nodetype=int)
filename = os.path.basename(graph_edgelist)
G.name = os.path.splitext(filename)[0]
args.remove(graph_edgelist)
outfile=args.pop()
if os.path.exists(outfile) and not options.force:
raise Exception("Output file " + outfile +
" exists. Won't overwrite without --force option.")
n = 0
histograms = []
for histfile in args:
f = open(histfile, 'rb')
histogram = pickle.load(f)
if not isinstance(histogram, collections.Mapping):
raise Exception('Object in ' + histfile +
' is not a dictionary: ' + str(type(histogram)))
if n == 0:
n = histogram['num_samples']
if histogram['num_samples'] != n:
raise Exception('inconsistent number of samples, '
'expected ' + str(n) + ', actual ' +
histogram['num_samples'])
del histogram['num_samples']
histograms.append(histogram)
nodes = G.nodes()
nodes.sort()
builder = ConsensusDendrogramBuilder()
C = builder.build(nodes, histograms, n)
# Save the consensus dendrogram to a GML file.
nx.write_gml(C, outfile)
print("Saved merged consensus dendrogram to " + outfile + ".")
return 0
def main():
parser = OptionParser(
description=
"Finds a consensus dendrogram from an HRG model of a network. Saves the consensus dendrogram to a graph markup language (GML) file. Saves the histogram of splits in the consensus dendrogram to a file in Python's pickle format.",
prog='hrg-consensus.py',
usage='%prog [options] GRAPH_EDGELIST_FILE DENDROGRAM_GML_FILE')
parser.add_option(
'-s',
'--num-samples',
action='store',
type=int,
default=10000,
help=
'The number of times to sample the dendrogram\'s splits (default=10000).'
)
parser.add_option('-t',
'--temperature',
action='store',
type=float,
default=2.0,
help='The temperature at which to run (default=2.0).')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.print_help()
return 1
graph_edgelist = args[0]
G = nx.read_edgelist(graph_edgelist, nodetype=int)
filename = os.path.basename(graph_edgelist)
G.name = os.path.splitext(filename)[0]
gml_file = args[1]
D = Dendrogram.from_gml_file(gml_file, G)
bestL = initL = D.graph['L']
bestI = 0
print_status("step", "L", "best L", "% complete", "consensus size")
threshold = 1 / (50.0 * G.number_of_nodes())
burnin = 200 * G.number_of_nodes()
i = 1
out = os.path.splitext(graph_edgelist)[0]
out += '-consensus-temp-%0.2f' % options.temperature
dendro_file = out + '-dendrogram.gml'
hist_file = out + '-histogram.dat'
print("HRG consensus dendrogram will be saved as " + dendro_file)
print("Split histogram will be saved as " + hist_file)
while D.num_samples < options.num_samples:
taken = D.monte_carlo_move(T=options.temperature, debug=False)
if i > burnin and random.random() < threshold:
D.sample_splits()
t = ''
if taken:
t = '*'
if D.graph['L'] > bestL:
bestL = D.graph['L']
if i % 4096 == 0:
nsplits = D.num_samples
pct_complete = 100 * D.num_samples / float(options.num_samples)
print_status("[" + str(i) + "]", "%.3f" % D.graph['L'],
"%.3f" % bestL, "%8.2f" % pct_complete,
"%10d" % nsplits)
if i % 10 == 0:
sys.stdout.flush()
i += 1
# Save the histogram to a file.
D.split_histogram['num_samples'] = D.num_samples
pickle.dump(D.split_histogram, open(hist_file, mode='wb'))
del D.split_histogram['num_samples']
print("Saved split histogram to " + hist_file)
# Build the consensus dendrogram, save it to a file.
builder = ConsensusDendrogramBuilder()
C = builder.build(D.graph_nodes_list, D.split_histogram, D.num_samples)
nx.write_gml(C, out + '-dendrogram.gml')
print("Saved consensus dendrogram to " + dendro_file)
return 0
def main():
parser = OptionParser(
description="Finds a consensus dendrogram from an HRG model of a network. Saves the consensus dendrogram to a graph markup language (GML) file. Saves the histogram of splits in the consensus dendrogram to a file in Python's pickle format.",
prog='hrg-consensus.py',
usage='%prog [options] GRAPH_EDGELIST_FILE DENDROGRAM_GML_FILE')
parser.add_option('-s', '--num-samples', action='store', type=int,
default=10000, help='The number of times to sample the dendrogram\'s splits (default=10000).')
parser.add_option('-t', '--temperature', action='store', type=float,
default=2.0, help='The temperature at which to run (default=2.0).')
(options, args) = parser.parse_args()
if len(args) != 2:
parser.print_help()
return 1
graph_edgelist=args[0]
G=nx.read_edgelist(graph_edgelist, nodetype=int)
filename=os.path.basename(graph_edgelist)
G.name=os.path.splitext(filename)[0]
gml_file=args[1]
D=Dendrogram.from_gml_file(gml_file, G)
bestL=initL=D.graph['L']
bestI=0
print_status("step", "L", "best L", "% complete", "consensus size")
threshold = 1/(50.0*G.number_of_nodes())
burnin = 200*G.number_of_nodes()
i=1
out = os.path.splitext(graph_edgelist)[0]
out += '-consensus-temp-%0.2f' % options.temperature
dendro_file = out + '-dendrogram.gml'
hist_file = out + '-histogram.dat'
print("HRG consensus dendrogram will be saved as " + dendro_file)
print("Split histogram will be saved as " + hist_file)
while D.num_samples < options.num_samples:
taken=D.monte_carlo_move(T=options.temperature, debug=False)
if i > burnin and random.random() < threshold:
D.sample_splits()
t = ''
if taken:
t = '*'
if D.graph['L'] > bestL:
bestL=D.graph['L']
if i % 4096 == 0:
nsplits = D.num_samples
pct_complete = 100 * D.num_samples / float(options.num_samples)
print_status(
"[" + str(i) + "]",
"%.3f" % D.graph['L'],
"%.3f" % bestL,
"%8.2f" % pct_complete,
"%10d" % nsplits)
if i % 10 == 0:
sys.stdout.flush()
i+=1
# Save the histogram to a file.
D.split_histogram['num_samples'] = D.num_samples
pickle.dump(D.split_histogram, open(hist_file, mode='wb'))
del D.split_histogram['num_samples']
print("Saved split histogram to " + hist_file)
# Build the consensus dendrogram, save it to a file.
builder = ConsensusDendrogramBuilder()
C = builder.build(D.graph_nodes_list, D.split_histogram, D.num_samples)
nx.write_gml(C, out + '-dendrogram.gml')
print("Saved consensus dendrogram to " + dendro_file)
return 0