def read_track(self, bedgraph, start=None, end=None, empty=np.nan, flank=None):
"""Read track values from BigWig file handle"""
if start:
self.start = start
if end:
self.end = end
if flank:
self.start = self.start - flank
self.end = self.end + flank
handle = BedGraphFile(bedgraph)
self.vals = handle.read(self.chrom, self.start, self.end, empty=empty)
handle.close()
def read_track(self, bedgraph, start = None, end = None, empty = np.nan, flank = None):
"""Read track values from BigWig file handle"""
if start:
self.start = start
if end:
self.end = end
if flank:
self.start = self.start - flank
self.end = self.end + flank
handle = BedGraphFile(bedgraph)
self.vals = handle.read(self.chrom, self.start,
self.end, empty = empty)
handle.close()
def _signalHelper(arg):
"""Get aggregate signal around a set of sites
"""
(chunks, params) = arg
bg = BedGraphFile(params.bg)
agg = np.zeros(params.up + params.down + 1)
if params.all:
counter = 0
mat = np.zeros((len(chunks), params.up + params.down + 1))
else:
agg = np.zeros(params.up + params.down + 1)
for chunk in chunks:
try:
chunk.center()
if params.up != 0 and params.down != 0:
chunk.slop(chromDict=params.chrs,
up=params.up,
down=params.down)
sig = bg.read(chunk.chrom, chunk.start, chunk.end)
if params.up != 0 and params.down != 0 and len(sig) != (
params.up + params.down + 1):
if chunk.start == 0:
sig = np.hstack(
(np.zeros(params.up + params.down + 1 - len(sig)),
sig))
else:
sig = np.hstack(
(sig,
np.zeros(params.up + params.down + 1 - len(sig))))
if chunk.strand == "-":
sig = sig[::-1]
if params.exp:
sig = np.exp(sig)
if params.positive:
sig[sig < 0] = 0
if params.scale:
tmp = sig
tmp[np.isnan(tmp)] = 0
sig = sig / (np.sum(abs(sig)) + (np.sum(abs(sig)) == 0))
if params.all:
mat[counter] = sig
counter += 1
else:
sig[np.isnan(sig)] = 0
agg += sig
except Exception as e:
print(
('Caught exception when processing:\n' + chunk.asBed() + "\n"))
traceback.print_exc()
print()
bg.close()
raise e
bg.close()
if params.all:
return mat
else:
return agg
def _signalHelper(arg):
"""Get aggregate signal around a set of sites
"""
(chunks, params) = arg
bg = BedGraphFile(params.bg)
agg = np.zeros(params.up + params.down + 1)
if params.all:
counter = 0
mat = np.zeros((len(chunks),params.up + params.down + 1))
else:
agg = np.zeros(params.up + params.down + 1)
for chunk in chunks:
try:
chunk.center()
if params.up!=0 and params.down!=0:
chunk.slop(chromDict = params.chrs, up = params.up, down = params.down)
sig = bg.read(chunk.chrom, chunk.start, chunk.end)
if params.up!=0 and params.down!=0 and len(sig) != (params.up + params.down + 1):
if chunk.start == 0:
sig = np.hstack((np.zeros(params.up + params.down + 1 - len(sig)),
sig))
else:
sig = np.hstack((sig,np.zeros(params.up + params.down + 1 - len(sig))))
if chunk.strand == "-":
sig = sig[::-1]
if params.exp:
sig = np.exp(sig)
if params.positive:
sig[sig<0]=0
if params.scale:
tmp = sig
tmp[np.isnan(tmp)]=0
sig = sig / (np.sum(abs(sig))+ (np.sum(abs(sig))==0))
if params.all:
mat[counter] = sig
counter += 1
else:
sig[np.isnan(sig)]=0
agg += sig
except Exception as e:
print('Caught exception when processing:\n' + chunk.asBed() + "\n")
traceback.print_exc()
print()
bg.close()
raise e
bg.close()
if params.all:
return mat
else:
return agg