def run(bam, track_file_name, window_size):
track = tb.openFile(track_file_name, "w")
track_name = bam.split(".bam")[0]
print(track_name)
test = checkIfNodeExists(track, track_name)
if test: return
bam_file = pysam.Samfile(bam)
chrs = bam_file.references
vals = []
chr_length = 0
start = 0
end = window_size
i = 0
for chr in chrs:
chr_length = bam_file.lengths[bam_file.references.index(chr)]
vals = np.zeros(chr_length / window_size)
print chr
#track_chr = track._f_getChild(chr_name)
print ">> Counting..."
while end < chr_length:
vals[i] = float(bam_file.count(reference=chr, start=start, end=end)) / bam_file.mapped
i += 1
start = start + window_size
end = end + window_size
print ">> Creating array..."
track.createArray("/" + track_name, chr, vals)
# out_track_chr = out.getNode("/" + out_track_name, chr_name)
track_util.setTrackAttributes(track, track_name + "/" + chr, 0, chr_length / window_size, chr, window_size)
# def setTrackAttributes(file, node, start, stop, name, resolution):
# for name in track_chr._v_attrs._f_list():
# out.etNodeAttr("/" + "/".join([out_track_name, chr_name]), name, track_chr._v_attrs[name])
print "Flushing..."
track.flush()
track.close()
def write_values(obj, pos_vect, chrom, chr_length):
if obj.output_type == "wig":
out = "fixedStep chrom={0} start={1} step={2} span={2}\n".format(
chrom, "1", obj.window_size)
obj.outfile.write(out)
for val in pos_vect:
obj.outfile.write(str(val) + "\n")
elif obj.output_type == "h5":
obj.outfile.createArray("/" + obj.track_name, chrom, pos_vect)
track_util.setTrackAttributes(obj.outfile,
obj.track_name + "/" + chrom, 0,
chr_length / obj.window_size, chrom,
obj.window_size)
def write_values(obj, pos_vect, chrom, chr_length):
if obj.output_type == "wig":
out = "fixedStep chrom={0} start={1} step={2} span={2}\n".format(chrom,
"1",
obj.window_size)
obj.outfile.write(out)
for val in pos_vect:
obj.outfile.write(str(val) + "\n")
elif obj.output_type == "h5":
obj.outfile.createArray("/" + obj.track_name, chrom, pos_vect)
track_util.setTrackAttributes(obj.outfile,
obj.track_name + "/" + chrom,
0,
chr_length / obj.window_size,
chrom,
obj.window_size)
