def getNucSignal(self):
"""Gets Nucleosome Signal Track"""
self.nuc_cov = CoverageTrack(self.chrom, self.start, self.end)
self.nuc_cov.calculateCoverage(self.mat, self.params.lower,
self.params.upper, self.params.window)
self.bias = BiasTrack(self.chrom, self.start, self.end)
self.bias.calculateBackgroundSignal(self.bias_mat, self.params.vmat,
self.nuc_cov)
self.nuc_signal = SignalTrack(self.chrom, self.start, self.end)
self.nuc_signal.calculateSignal(self.mat, self.params.vmat)
self.norm_signal = NormSignalTrack(self.chrom, self.start, self.end)
self.norm_signal.calculateNormSignal(self.nuc_signal, self.bias)
def calculateBackgroundSignal(self, mat, vmat, nuc_cov):
offset=self.start-mat.start-vmat.w
if offset<0:
raise Exception("Insufficient flanking region on \
mat to calculate signal")
self.vmat = vmat
self.bias_mat = mat
self.cov = CoverageTrack(self.chrom, self.start, self.end)
self.cov.calculateCoverage(self.bias_mat, vmat.lower,
vmat.upper, vmat.w*2+1)
self.nuc_cov = nuc_cov.vals
self.vals = signal.correlate(self.bias_mat.get(vmat.lower,vmat.upper,
self.bias_mat.start + offset,
self.bias_mat.end - offset),
vmat.mat,mode = 'valid')[0]
self.vals = self.vals * self.nuc_cov/ self.cov.vals
def _covHelper(arg):
"""Computes coverage track for a particular set of bed regions"""
(chunk, args) = arg
try:
offset = args.window // 2
mat = FragmentMat2D(chunk.chrom, chunk.start - offset,
chunk.end + offset, args.lower, args.upper,
args.atac)
mat.makeFragmentMat(args.bam)
cov = CoverageTrack(chunk.chrom, chunk.start, chunk.end)
cov.calculateCoverage(mat,
lower=args.lower,
upper=args.upper,
window_len=args.window)
cov.vals *= args.scale / float(args.window)
except Exception as e:
print(('Caught exception when processing:\n' + chunk.asBed() + "\n"))
traceback.print_exc()
print()
raise e
return cov
def getCov(self):
"""Get read coverage for regions"""
self.cov = CoverageTrack(self.chrom, self.start, self.end)
self.cov.calculateCoverage(self.mat, 0, self.params.upper, self.params.window)
def getNFR(self):
"""get number of reads of sub-nucleosomal length"""
self.nfr_cov = CoverageTrack(self.chrom, self.start, self.end)
self.nfr_cov.calculateCoverage(self.mat, 0, self.params.lower,
self.params.window)
