def callPeaks(self):
"""Call peaks of occupancy profile"""
peaks = call_peaks(self.occ.smoothed_vals, sep = self.params.sep, min_signal = self.params.min_occ)
for peak in peaks:
tmp = OccPeak(peak + self.start, self)
if tmp.occ_lower > self.params.min_occ and tmp.reads > 0:
self.peaks[peak] = tmp
def findAllNucs(self):
"""Find peaks in data"""
self.nuc_collection = {}
combined = self.norm_signal.vals + self.smoothed.vals
#find peaks in normalized sigal
cands1 = call_peaks(combined,
min_signal=0,
sep=self.params.redundant_sep,
boundary=self.params.nonredundant_sep // 2,
order=self.params.redundant_sep // 2)
for i in cands1:
nuc = Nucleosome(i + self.start, self)
if nuc.nuc_cov > self.params.min_reads:
nuc.getLR(self)
if nuc.lr > self.params.min_lr:
nuc.getZScore(self)
if nuc.z >= self.params.min_z:
nuc.getOcc(self)
self.nuc_collection[i] = nuc
self.sorted_nuc_keys = np.array(sorted(self.nuc_collection.keys()))
self.nonredundant = reduce_peaks(
self.sorted_nuc_keys,
[self.nuc_collection[x].z
for x in self.sorted_nuc_keys], self.params.nonredundant_sep)
self.redundant = np.setdiff1d(self.sorted_nuc_keys, self.nonredundant)
def findAllNucs(self):
"""Find peaks in data"""
self.nuc_collection = {}
combined = self.norm_signal.vals + self.smoothed.vals
# find peaks in normalized sigal
cands1 = call_peaks(
combined,
min_signal=0,
sep=self.params.redundant_sep,
boundary=self.params.nonredundant_sep / 2,
order=self.params.redundant_sep / 2,
)
for i in cands1:
nuc = Nucleosome(i + self.start, self)
if nuc.nuc_cov > self.params.min_reads:
nuc.getLR(self)
if nuc.lr > self.params.min_lr:
nuc.getZScore(self)
if nuc.z >= self.params.min_z:
nuc.getOcc(self)
self.nuc_collection[i] = nuc
self.sorted_nuc_keys = np.array(sorted(self.nuc_collection.keys()))
self.nonredundant = reduce_peaks(
self.sorted_nuc_keys,
map(lambda x: self.nuc_collection[x].z, self.sorted_nuc_keys),
self.params.nonredundant_sep,
)
self.redundant = np.setdiff1d(self.sorted_nuc_keys, self.nonredundant)
def test_call_peaks_case1(self):
"""test case1 for call_peaks"""
peaks = call_peaks(np.array([1, 2, 3, 2, 1, 4, 1, 2, 1, 0, 0]),
min_signal=1,
sep=3)
self.assertTrue(np.array_equal(peaks, np.array([2, 5])))
def test_call_peaks_case1(self):
"""test case1 for call_peaks"""
peaks = call_peaks(np.array([1,2,3,2,1,4,1,2,1,0,0]),min_signal=1,sep=3)
self.assertTrue(np.array_equal(peaks,np.array([2,5])))
