def _insHelper(arg):
(chunk, args) = arg
try:
ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
ins.calculateInsertions( args.bam, lower = args.lower, upper = args.upper, atac = args.atac)
except Exception as e:
print('Caught exception when processing:\n'+ chunk.asBed()+"\n")
traceback.print_exc()
print()
raise e
return ins
def test_ins_methods(self):
"""test that two methods for getting insertion track give same result"""
ins1 = InsertionTrack(self.chunk.chrom, self.chunk.start, self.chunk.end)
ins1.calculateInsertions("example/single_read.bam")
mat = FragmentMat2D(self.chunk.chrom, self.chunk.start, self.chunk.end, 0, 100)
mat.makeFragmentMat("example/single_read.bam")
ins2 = mat.getIns()
self.assertTrue(
np.array_equal(
ins1.get(self.chunk.start + 100, self.chunk.start + 300),
ins2.get(self.chunk.start + 100, self.chunk.start + 300),
)
)
def test_ins_methods(self):
"""test that two methods for getting insertion track give same result"""
ins1 = InsertionTrack(self.chunk.chrom, self.chunk.start,
self.chunk.end)
ins1.calculateInsertions('example/single_read.bam')
mat = FragmentMat2D(self.chunk.chrom, self.chunk.start, self.chunk.end,
0, 100)
mat.makeFragmentMat('example/single_read.bam')
ins2 = mat.getIns()
self.assertTrue(
np.array_equal(
ins1.get(self.chunk.start + 100, self.chunk.start + 300),
ins2.get(self.chunk.start + 100, self.chunk.start + 300)))
def _insHelperSmooth(arg):
"""Computes smoothed insertion track for a particular set of bed regions"""
(chunk, args) = arg
try:
offset = args.smooth / 2
ins = InsertionTrack(chunk.chrom, chunk.start - offset, chunk.end + offset)
ins.calculateInsertions( args.bam, lower = args.lower, upper = args.upper, atac = args.atac)
ins.smooth_track(args.smooth, window = "gaussian", mode= 'valid')
except Exception as e:
print('Caught exception when processing:\n'+ chunk.asBed()+"\n")
traceback.print_exc()
print()
raise e
return ins
def _insHelper(arg):
(chunk, args) = arg
try:
ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
ins.calculateInsertions(args.bam,
lower=args.lower,
upper=args.upper,
atac=args.atac)
except Exception as e:
print('Caught exception when processing:\n' + chunk.asBed() + "\n")
traceback.print_exc()
print()
raise e
return ins
def getIns(self):
"""Collape matrix into insertions. Will reduce span on chromosome"""
pattern = np.zeros(
(self.upper - self.lower, self.upper + (self.upper - 1) % 2))
mid = self.upper / 2
for i in range(self.lower, self.upper):
pattern[i - self.lower, mid + (i - 1) / 2] = 1
pattern[i - self.lower, mid - (i / 2)] = 1
ins = signal.correlate2d(self.mat, pattern, mode="valid")[0]
insertion_track = InsertionTrack(self.chrom,
self.start + pattern.shape[1] / 2,
self.end - (pattern.shape[1] / 2))
insertion_track.assign_track(ins)
return insertion_track
def _pwmHelper(arg):
""""Helper function for multiprocessing acquisition of sequence around insertions"""
(chunks, params) = arg
try:
n = 0.0
mat = np.zeros((len(params.nucleotides), params.up + params.down + 1))
for chunk in chunks:
ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
if params.sym:
ins.calculateInsertions(params.bam,
lower=params.lower,
upper=params.upper,
atac=params.atac)
mat += ins.getInsertionSequences(params.fasta,
params.nucleotides,
up=params.up,
down=params.down)
else:
ins.calculateStrandedInsertions(params.bam,
lower=params.lower,
upper=params.upper,
atac=params.atac)
mat += ins.getStrandedInsertionSequences(params.fasta,
params.nucleotides,
up=params.up,
down=params.down)
n += sum(ins.vals)
except Exception as e:
print('Caught exception when processing:\n' + chunk.asBed() + "\n")
traceback.print_exc()
print()
raise e
return mat, n
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 _pwmHelper(arg):
""""Helper function for multiprocessing acquisition of sequence around insertions"""
(chunks, params) = arg
try:
n = 0.0
mat = np.zeros((len(params.nucleotides), params.up + params.down + 1))
for chunk in chunks:
ins = InsertionTrack(chunk.chrom, chunk.start, chunk.end)
if params.sym:
ins.calculateInsertions( params.bam, lower = params.lower, upper = params.upper, atac = params.atac)
mat += ins.getInsertionSequences(params.fasta, params.nucleotides, up = params.up, down = params.down)
else:
ins.calculateStrandedInsertions( params.bam, lower = params.lower, upper = params.upper, atac = params.atac)
mat += ins.getStrandedInsertionSequences(params.fasta, params.nucleotides, up = params.up, down = params.down)
n += sum(ins.vals)
except Exception as e:
print('Caught exception when processing:\n'+ chunk.asBed()+"\n")
traceback.print_exc()
print()
raise e
return mat, n
def _insHelperSmooth(arg):
"""Computes smoothed insertion track for a particular set of bed regions"""
(chunk, args) = arg
try:
offset = args.smooth / 2
ins = InsertionTrack(chunk.chrom, chunk.start - offset,
chunk.end + offset)
ins.calculateInsertions(args.bam,
lower=args.lower,
upper=args.upper,
atac=args.atac)
ins.smooth_track(args.smooth, window="gaussian", mode='valid')
except Exception as e:
print('Caught exception when processing:\n' + chunk.asBed() + "\n")
traceback.print_exc()
print()
raise e
return ins