def __init__(self, bamname, outname, track_name,
window_size, extend, pe, pseudo,
ends, smooth, norm_by_mean, no_norm, output_type):
self.bamname = bamname
self.bamfile = pysam.AlignmentFile(bamname, 'rb')
self.outname = outname
self.output_type = output_type
self.outfile = ""
self.track_name = track_name
if output_type == "wig":
self.outfile = open(outname, 'w')
elif output_type == "h5":
self.outfile = tb.openFile(outname, "a")
test = track_util.checkIfNodeExists(self.outfile, self.track_name,
create=True, accept_existence=False)
if test: sys.exit()
elif output_type == "none":
pass
self.window_size = atoi(window_size)
self.pe = pe
self.extend = int(extend)
self.nreads = self.bamfile.mapped
self.pseudo = pseudo
self.ends = ends
self.smooth = smooth
self.norm_by_mean = norm_by_mean
self.no_norm = no_norm
#pdb.set_trace()
self.window_correct = {}
self.norm_path = ".".join([bamname, "chr_means_0"])
if os.path.exists(self.norm_path):
for line in open(self.norm_path, 'r'):
sline = line.split()
self.window_correct[sline[0]] = float(sline[1])
if pe:
# If strand separated BAM
if re.search("plus", bamname) or re.search("minus", bamname):
self.nreads = self.bamfile.mapped
# Normalize to number of fragments
else:
self.nreads = self.bamfile.mapped / 2
else:
self.nreads = self.bamfile.mapped
print self.nreads
self.chr_lengths = self.bamfile.lengths
self.chrs_queue = []
for index in range(self.bamfile.nreferences):
self.chrs_queue.append((self.bamfile.references[index], self.bamfile.lengths[index]))
def run(self):
out_track_name = self.in_track._v_name
print out_track_name
test = tutil.checkIfNodeExists(self.out_track, out_track_name)
if test: return
for chr in self.in_track._f_iterNodes():
chr_name = chr._v_name
print chr_name
track_chr = self.in_track._f_getChild(chr_name)
out_track_chr = self.int_normalize(track_chr)
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 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 run(self):
# various machinations to keep last name component last
track_name_split = self.in_track._v_name.split("_")
out_track_name = "_".join(["_".join(track_name_split[0:-1]), "dampen" + str(self.dampen), track_name_split[-1]])
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
track_chr = self.in_track._f_getChild(chr_name)
cutoff = self.dampen * np.std(track_chr[:])
mask = ~(np.abs(track_chr[:] - np.mean(track_chr[:])) < cutoff)
out_track_chr = track_chr[:]
out_track_chr[mask] = cutoff
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 __init__(self, bamname, outname, track_name, window_size, extend, pe,
pseudo, ends, smooth, norm_by_mean, no_norm, output_type):
self.bamname = bamname
self.bamfile = pysam.Samfile(bamname, 'rb')
self.outname = outname
self.output_type = output_type
self.outfile = ""
self.track_name = track_name
if output_type == "wig":
self.outfile = open(outname, 'w')
elif output_type == "h5":
self.outfile = tb.openFile(outname, "a")
test = track_util.checkIfNodeExists(self.outfile,
self.track_name,
create=True,
accept_existence=False)
if test: sys.exit()
elif output_type == "none":
pass
self.window_size = atoi(window_size)
self.pe = pe
self.extend = int(extend)
self.nreads = self.bamfile.mapped
# self.bed_name = bed
# self.bed_file = ""
# if bed:
# self.bed_file = open(bed)
self.pseudo = pseudo
# self.full = full
self.ends = ends
self.smooth = smooth
self.norm_by_mean = norm_by_mean
self.no_norm = no_norm
#pdb.set_trace()
self.window_correct = {}
self.norm_path = ".".join([bamname, "chr_means_0"])
if os.path.exists(self.norm_path):
for line in open(self.norm_path, 'r'):
sline = line.split()
self.window_correct[sline[0]] = float(sline[1])
if pe:
# If strand separated BAM
if re.search("plus", bamname) or re.search("minus", bamname):
self.nreads = self.bamfile.mapped
# Normalize to number of fragments
else:
self.nreads = self.bamfile.mapped / 2
else:
self.nreads = self.bamfile.mapped
print self.nreads
self.chr_lengths = self.bamfile.lengths
self.chrs_queue = []
for index in range(self.bamfile.nreferences):
self.chrs_queue.append(
(self.bamfile.references[index], self.bamfile.lengths[index]))