def makeSmoothed(self, window_len = 121, sd = 20):
self.smoothed_vals = smooth(self.vals, window_len, window = "gaussian", sd = sd,
mode = "same", norm = True)
self.smoothed_lower = smooth(self.lower_bound, window_len, window = "gaussian", sd = sd,
mode = "same", norm = True)
self.smoothed_upper = smooth(self.upper_bound, window_len, window = "gaussian", sd = sd,
mode = "same", norm = True)
def smooth_track(self, window_len, window="flat", sd=None, mode="valid", norm=True):
""" smoothing of track"""
self.smoothed = True
self.vals = smooth(self.vals, window_len, window=window, sd=sd, mode=mode, norm=norm)
if mode == "valid":
self.start = self.start + window_len / 2
self.end = self.end - window_len / 2
def smooth_track(self, window_len, window='flat', sd = None,
mode = 'valid', norm = True):
""" smoothing of track"""
self.smoothed=True
self.vals = smooth(self.vals, window_len, window = window, sd = sd,
mode = mode, norm = norm)
if mode == 'valid':
self.start = self.start + window_len/2
self.end = self.end - window_len/2
def getLocalbias(self, windowlen = 55, window = "flat"):
"""Make bias a reflection of score in a given window"""
if self.log:
ebias = np.exp(self.vals)
else:
ebias = self.vals
smoothed = smooth(ebias,windowlen, window, norm = False)
flank = windowlen/2
if self.log:
self.vals = np.log(ebias[flank:-flank]/(smoothed-ebias[flank:-flank]))
else:
self.vals = ebias[flank:-flank]/(smoothed-ebias[flank:-flank])
self.start = self.start + flank
self.end = self.end - flank
def calculateCoverageSmooth(self,mat,lower,upper,window_len,sd):
"""Compute coverage of fragment centers using gaussia window"""
offset=self.start-mat.start-(window_len/2)
if offset<0:
raise Exception("Insufficient flanking region on \
mat to calculate coverage with desired window")
lower=lower-mat.lower
upper=upper-mat.lower
if offset!=0:
collapsed = np.sum(mat.mat[lower:upper,offset:-offset],axis=0)
else:
collapsed = np.sum(mat.mat[lower:upper,],axis=0)
self.vals = smooth(collapsed, window_len, sd= sd, window="gaussian",
mode='valid',norm=False)
def getLocalbias(self, windowlen = 55, window = "flat"):
"""Make bias a reflection of score in a given window"""
if self.log:
ebias = np.exp(self.vals)
else:
ebias = self.vals
smoothed = smooth(ebias,windowlen, window, norm = False)
flank = windowlen/2
if self.log:
self.vals = np.log(ebias[flank:-flank]/(smoothed-ebias[flank:-flank]))
else:
self.vals = ebias[flank:-flank]/(smoothed-ebias[flank:-flank])
self.start = self.start + flank
self.end = self.end - flank
def calculateCoverageSmooth(self, mat, lower, upper, window_len, sd):
"""Compute coverage of fragment centers using gaussia window"""
offset = self.start - mat.start - (window_len / 2)
if offset < 0:
raise Exception(
"Insufficient flanking region on \
mat to calculate coverage with desired window"
)
lower = lower - mat.lower
upper = upper - mat.lower
if offset != 0:
collapsed = np.sum(mat.mat[lower:upper, offset:-offset], axis=0)
else:
collapsed = np.sum(mat.mat[lower:upper,], axis=0)
self.vals = smooth(collapsed, window_len, sd=sd, window="gaussian", mode="valid", norm=False)
