def getOcc(self):
"""gets occupancy track-- reads in from bedgraph"""
self.occ = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ.read_track(self.params.occ_track)
#lower_file = self.params.occ_track[:-11] + 'lower_bound.bedgraph.gz'
#self.occ_lower = Track(self.chrom,self.start,self.end,"Occupancy")
#self.occ_lower.read_track(lower_file)
upper_file = self.params.occ_track[:-11] + 'upper_bound.bedgraph.gz'
self.occ_upper = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ_upper.read_track(upper_file)
def getOcc(self):
"""gets occupancy track-- either reads in from bw handle given, or makes new"""
self.occ = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ.read_track(self.params.occ_track)
lower_file = self.params.occ_track[:-11] + 'lower_bound.bedgraph.gz'
self.occ_lower = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ_lower.read_track(lower_file)
upper_file = self.params.occ_track[:-11] + 'upper_bound.bedgraph.gz'
self.occ_upper = Track(self.chrom, self.start, self.end, "Occupancy")
self.occ_upper.read_track(upper_file)
def getIns(self):
"""gets insertion track-- reads in from bedgraph"""
if self.params.ins_track is None:
self.ins = InsertionTrack(self.chrom, self.start, self.end)
self.ins.calculateInsertions(self.params.bam)
else:
self.ins = Track(self.chrom, self.start, self.end, "Insertion")
self.ins.read_track(self.params.ins_track)
def fit(self):
x = np.linspace(0,self.length() -1, self.length())
fit = np.zeros(self.length())
for nuc in self.sorted_nuc_keys:
self.nuc_collection[nuc].getFuzz(self)
fit += norm(x,self.nuc_collection[nuc].fuzz**2, self.nuc_collection[nuc].weight, self.nuc_collection[nuc].fit_pos)
self.fitted = Track(self.chrom, self.start, self.end,
"Fitted Nucleosome Signal")
self.fitted.assign_track(fit)
def smoothSignal(self):
"""Smooth thenormalized signal track"""
window_len = 6 * self.params.smooth_sd + 1
self.smoothed = Track(self.chrom,self.start,self.end, "Smooth Signal")
tmp = copy(self.norm_signal.vals)
self.smoothed.assign_track(tmp)
self.smoothed.vals[ self.smoothed.vals < 0] = 0
self.smoothed.smooth_track(window_len, window = "gaussian",
sd = self.params.smooth_sd, mode = 'same',
norm = True)
def test_read_and_get(self):
"""test the read and get functionality of track class"""
track = Track(self.chunk.chrom, self.chunk.start, self.chunk.end)
track.read_track('example/example.Scores.bedgraph.gz')
val = 1.35994655714
self.assertTrue(abs(val - track.get(pos=706661)) < 0.001)
