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cluster.py
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cluster.py
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"""
Module cluster
"""
import sys
from helpers import WindowState
from helpers import flat_windows_rd_from_indexes
from helpers import MixedWindowView
from pomegranate import*
from helpers import WindowType
from helpers import WARNING
from preprocess_utils import compute_statistic
from preprocess_utils import get_distance_metric
class Cluster(object):
@staticmethod
def load(filename):
with open(filename, 'r') as f:
idx = int(f.readline().split(":")[1].rstrip("\n"))
indices = list(f.readline().split(":")[1].rstrip("\n"))
center = int(f.readline().split(":")[1].rstrip("\n"))
cluster = Cluster(id_=idx, indexes=indices,
windows=None, center_idx=center,
dist_metric=None)
diameter = f.readline().split(":")[1].rstrip("\n")
if diameter != '-inf':
diameter = float(diameter)
cluster.diameter = diameter
mean = float(f.readline().split(":")[1].rstrip("\n"))
std = float(f.readline().split(":")[1].rstrip("\n"))
cluster.wga_mean = mean
cluster.wga_std = std
mean = float(f.readline().split(":")[1].rstrip("\n"))
std = float(f.readline().split(":")[1].rstrip("\n"))
cluster.no_wga_mean = mean
cluster.no_wga_std = std
other_clusts = int(f.readline().split(":")[1].rstrip("\n"))
if other_clusts >0 :
dist_from_others={}
for lidx in range(other_clusts):
line = f.readline().split(":")
indeces = line[0].split(",")
idx1 = int(indeces[0])
idx2 = int(indeces[1])
value = float(line[1].rstrip("\n"))
if idx1 != idx:
raise Error("id {0} should have been "
"equal to cluster id {1} ".format(idx1, idx))
dist_from_others[(idx1,idx2)]=value
cluster.distance_from_others = dist_from_others
return cluster
@staticmethod
def dbi(clusters):
r={}
for ci in clusters:
for cj in clusters:
si = ci.diameter
sj = cj.diameter
dij = ci.distance_from_other(other=cj)
r[(ci.cidx, cj.cidx)] = (si+sj)/dij
# for each cluster find the maximum
maxs = []
for ci in clusters:
max_ci = 0.0
for cj in clusters:
if r[(ci.cidx, cj.cidx)] > max_ci:
max_ci = r[(ci.cidx, cj.cidx)]
maxs.append(max_ci)
return sum(maxs)/len(clusters)
def __init__(self, id_, indexes, windows,
center_idx, dist_metric):
self._id = id_
self._indexes = indexes
self._windows = windows,
self._center_idx = center_idx
self._dist_metric = dist_metric
self._state = WindowState.INVALID
self._wga_density = None
self._wga_mean = 0.0
self._wga_std = 0.0
self._no_wga_density = None
self._no_wga_mean = 0.0
self._no_wga_std=0.0
self._diameter = None
self._distance_from_others=None
@property
def state(self):
return self._state
@state.setter
def state(self, value):
self._state = value
@property
def cidx(self):
return self._id
@property
def indexes(self):
return self._indexes
@property
def center_idx(self):
return self._center_idx
@property
def center(self):
return self._windows[self._center_idx]
@property
def wga_density(self):
return self._wga_density
@wga_density.setter
def wga_density(self, value):
self._wga_density = value
@property
def wga_mean(self):
return self._wga_mean
@wga_mean.setter
def wga_mean(self, value):
self._wga_mean = value
@property
def wga_std(self):
return self._wga_std
@wga_std.setter
def wga_std(self, value):
self._wga_std = value
@property
def no_wga_density(self):
return self._no_wga_density
@no_wga_density.setter
def no_wga_density(self, value):
self._no_wga_density = value
@property
def no_wga_mean(self):
return self._no_wga_mean
@no_wga_mean.setter
def no_wga_mean(self, value):
self._no_wga_mean = value
@property
def no_wga_std(self):
return self._no_wga_std
@no_wga_std.setter
def no_wga_std(self, value):
self._no_wga_std = value
@property
def windows(self):
return self._windows
@property
def diameter(self):
if self._diameter is not None:
return self._diameter
return self.calculate_diameter()
@diameter.setter
def diameter(self, value):
self._diameter = value
@property
def distance_from_others(self):
return self._distance_from_others
@distance_from_others.setter
def distance_from_others(self, value):
self._distance_from_others = value
def calculate_diameter(self):
if self._windows is None:
raise Error("Cannot calculate cluster "
"diameter without windows. "
"Cluster id is {0}".format(self.cidx))
distance = 0.0
for i in self._indexes:
for j in self._indexes:
w1 = self._windows[i]
w2 = self._windows[j]
if w1.is_n_window() or w2.is_n_window():
continue
w1_wga_mean, w1_no_wga_mean = w1.get_rd_stats(statistics="mean",
name=WindowType.BOTH)
w2_wga_mean, w2_no_wga_mean = w2.get_rd_stats(statistics="mean",
name=WindowType.BOTH)
metric = get_distance_metric(self._dist_metric, degree=4)
new_dist = metric([w1_wga_mean, w1_no_wga_mean], [w2_wga_mean, w2_no_wga_mean])
if new_dist > distance:
distance = new_dist
self._diameter = distance
return distance
def get_distance_from_other(self, other):
if self._distance_from_others is None:
return "-inf"
if (self.cidx, other.cidx) not in self._distance_from_others:
return False
return self._distance_from_others[(self.cidx, other.cidx)]
def set_distance_from_other(self, other, dist):
if self._distance_from_others is None:
self._distance_from_others = {(self.cidx,other.cidx):dist}
else:
self._distance_from_others[(self.cidx,other.cidx)] = dist
def calculate_distance_from_other(self, other):
if other.cidx == self.cidx:
self.set_distance_from_other(other, 0.0)
return 0.0
if self._distance_from_others is not None and \
(self.cidx, other.cidx) in self._distance_from_others:
return self._distance_from_others[(self.cidx, other.cidx)]
if other.get_distance_from_other(other=self) != '-inf' or\
other.get_distance_from_other(other=self) != False:
self.set_distance_from_other(other,
other.get_distance_from_other(other=self))
return other.get_distance_from_other(other=self)
distance = sys.float_info.max
for i in self._indexes:
for j in other.indexes:
this_w = self._windows[i]
other_w = self._windows[j]
if this_w.is_n_window() or other_w.is_n_window():
continue
w1_wga_mean, w1_no_wga_mean = this_w.get_rd_stats(statistics="mean",
name=WindowType.BOTH)
w2_wga_mean, w2_no_wga_mean = other_w.get_rd_stats(statistics="mean",
name=WindowType.BOTH)
metric = get_distance_metric(self._dist_metric, degree=4)
new_dist = metric([w1_wga_mean, w1_no_wga_mean], [w2_wga_mean, w2_no_wga_mean])
if new_dist < distance:
distance = new_dist
self.set_distance_from_other(other=other, dist=distance)
return distance
def merge(self, cluster):
self._indexes.extend(cluster.indexes)
def save(self):
with open("cluster_" + str(self.cidx) + ".txt", 'w') as f:
f.write("ID:"+str(self.cidx) +"\n")
f.write("Indices:" + str(self.indexes) +"\n")
f.write("Center:" + str(self._center_idx) +"\n")
diam = str(self._diameter) if self._diameter is not None else '-inf'
f.write("Diameter: " + diam + "\n")
f.write("WGA_MEAN:"+str(self.wga_mean) +"\n")
f.write("WGA_STD:" + str(self.wga_std) +"\n")
f.write("NO_WGA_MEAN:" + str(self.no_wga_mean) +"\n")
f.write("NO_WGA_STD:" + str(self.no_wga_std) +"\n")
if self._distance_from_others is None:
f.write("N_DIST_OTHERS:" + str(0) +"\n")
else:
f.write("N_DIST_OTHERS:" + str(len(self._distance_from_others)) +"\n")
for item in self._distance_from_others:
f.write(str(item[0]) + "," + str(item[1])+":" + str(self._distance_from_others[item]) +"\n")
def get_sequence(self, size, window_type):
sequence =[]
if size < len(self._indexes):
counter = 0
for idx in self._indexes:
window = self._windows[idx]
sequence.append(window.get_rd_stats(statistics="mean"),
name=window_type)
counter +=1
if counter == size:
break
else:
print("{0} Cluster size is less than {1}".format(WARNING, size))
for idx in self._indexes:
window = self._windows[idx]
sequence.append(window.get_rd_stats(statistics="mean"),
name=window_type)
return sequence
def get_region_as_sequences(self, size, window_type, n_seqs):
sequences = []
sequence_local=[]
for idx in self._indexes:
window = self._windows[idx]
sequence_local.append(window.get_rd_stats(statistics="mean", name=window_type))
if len(sequence_local) == size:
sequences.append(sequence_local)
sequence_local=[]
if n_seqs is not None and len(sequences) == n_seqs:
break
return sequences
def get_statistics(self, statistic, window_type, **kwargs):
if window_type == WindowType.BOTH:
for index in self._indexes:
window = self._windows[index]
statistic1, statistic2 = \
window.get_rd_stats(statistics=statistic)
return statistic1, statistic2
else:
wga_windows = [window.get_window(window_type)
for window in self._windows]
window_data = flat_windows_rd_from_indexes(indexes=self._indexes,
windows=wga_windows)
return compute_statistic(data=window_data,statistics=statistic)
def get_window_statistics(self, statistic, **kwargs):
statistics = []
for idx in self.indexes:
window = self._windows[idx]
if isinstance(window, MixedWindowView):
statistics.append(window.get_rd_stats(name=kwargs["window_type"],
statistics=statistic))
else:
statistics.append(window.get_rd_stats(statistics=statistic))
return statistics