def window_core(obj, chrom):
bamfile = pysam.AlignmentFile(obj.bamname, 'rb')
chr_length = chrom[1]
chrom = chrom[0]
print chrom
pos_vect = np.zeros((chr_length / obj.window_size,))
read_mid = 0
# Loop through BAM reads, adding midpoints to position vector
for read in bamfile.fetch(chrom):
read_mid = sam.read_mid_compute(obj, read)
if read_mid < 0: continue
read_mid_index = read_mid / obj.window_size
if read_mid_index <= len(pos_vect) - 1:
pos_vect[read_mid_index] = pos_vect[read_mid_index] + 1
# Pseudocount 0 windows
if obj.pseudo:
pos_vect[pos_vect==0] = 1
# Normalize by Reads per million and by reads per kilobase
#window_correct = 1e6 * 1e3 / (float(obj.window_size) * obj.nreads)
# Normalize by Reads per million
window_correct = 1e6 * obj.nreads
pos_vect = window_correct * pos_vect
if obj.smooth > 0:
pos_vect = signal_utils.smooth(pos_vect, obj.smooth, window="flat")
if not obj.output_type == "none":
write_values(obj, pos_vect, chrom, chr_length)
def window_core(obj, chrom):
bamfile = pysam.Samfile(obj.bamname, 'rb')
#pdb.set_trace()
chr_length = chrom[1]
chrom = chrom[0]
print chrom
pos_vect = np.zeros((chr_length / obj.window_size, ))
read_mid = 0
# Loop through BAM reads, adding midpoints to position vector
for read in bamfile.fetch(chrom):
read_mid = sam.read_mid_compute(obj, read)
if read_mid < 0: continue
read_mid_index = read_mid / obj.window_size
if read_mid_index <= len(pos_vect) - 1:
pos_vect[read_mid_index] = pos_vect[read_mid_index] + 1
# Pseudocount 0 windows
if obj.pseudo:
pos_vect[pos_vect == 0] = 1
# Normalize by Reads per million and by reads per kilobase
window_correct = 1e6 * 1e3 / (float(obj.window_size) * obj.nreads)
pos_vect = window_correct * pos_vect
if obj.smooth > 0:
pos_vect = signal_utils.smooth(pos_vect, obj.smooth, window="flat")
if not obj.output_type == "none":
write_values(obj, pos_vect, chrom, chr_length)
def run(self):
out_track_name = self.in_track._v_name + "_smooth" + str(self.smooth)
print out_track_name
#pdb.set_trace()
test = tutil.checkIfNodeExists(self.out_track, out_track_name, True, False)
if test: return
for chrom in self.in_track._f_iterNodes():
chr_name = chrom._v_name
print chr_name
if chr_name == "unknown": continue
track_chr = self.in_track._f_getChild(chr_name)
out_track_chr = signal_utils.smooth(track_chr[:], self.smooth, window="flat")
self.out_track.createArray("/" + out_track_name, chr_name, out_track_chr)
for name in track_chr._v_attrs._f_list():
self.out_track.setNodeAttr("/" + "/".join([out_track_name, chr_name]), name, track_chr._v_attrs[name])
def window_core(obj, chrom):
bamfile = pysam.Samfile(obj.bamname, 'rb')
#pdb.set_trace()
chr_length = chrom[1]
chrom = chrom[0]
print chrom
# Normalize by Reads per million and by reads per kilobase
window_correct = 1e6 * 1e3 / (float(obj.window_size) * obj.nreads)
pos_vect = np.zeros((chr_length / obj.window_size,))
read_mid = 0
for read in bamfile.fetch(chrom):
read_mid = sam.read_mid_compute(obj, read)
if read_mid < 0: continue
read_mid_index = read_mid / obj.window_size
if read_mid_index <= len(pos_vect) - 1:
pos_vect[read_mid_index] = pos_vect[read_mid_index] + 1
out = "fixedStep chrom={0} start={1} step={2} span={2}\n".format(chrom, "1", obj.window_size)
obj.wigfile.write(out)
if obj.no_norm:
for val in pos_vect:
if obj.pseudo and val == 0: val = 1
obj.wigfile.write(str(val) + "\n")
pos_vect = window_correct * pos_vect
#pdb.set_trace()
if obj.smooth > 0:
pos_vect = signal_utils.smooth(pos_vect, obj.smooth, window="flat")
if not obj.no_output:
if obj.pseudo: pos_vect[pos_vect==0] = 1
if not obj.no_norm:
pos_vect = window_correct * pos_vect
for val in pos_vect:
obj.wigfile.write(str(val) + "\n")
