def main():
if len(sys.argv) < 3:
sys.stderr.write("Extract data for all chromosomes from a wiggle file.\n")
sys.stderr.write("need 2 paras: %s <wig> <output_prefix>\n" % os.path.basename(sys.argv[0]))
sys.exit(1)
wigfhd = open(sys.argv[1])
prefix = sys.argv[2]
wigtrack = WiggleIO.WiggleIO(wigfhd).build_wigtrack()
wigtrack.sort()
for chrom in wigtrack.get_chr_names():
wig_chr = wigtrack.get_data_by_chr(chrom)
newwigtrack = WigTrackI()
newwigtrack.span = wigtrack.span
(wig_chr_p,wig_chr_s) = wig_chr
for i in range(len(wig_chr_p)):
newwigtrack.add_loc(chrom,wig_chr_p[i],wig_chr_s[i])
newwigfile = sys.argv[2]+"."+chrom+".wig"
newwigfhd = open(newwigfile,"w")
newwigtrack.write_wig(newwigfhd,name="for chromosome %s" % chrom)
newwigfhd.close()
def main():
if len(sys.argv) < 4:
sys.stderr.write(
"Extract data for certain chromosome from a wiggle file.\n")
sys.stderr.write("need 3 paras: %s <chr> <wig> <newwig>\n" %
os.path.basename(sys.argv[0]))
sys.exit(1)
chrom = sys.argv[1]
wigfhd = open(sys.argv[2])
wigtrack = WiggleIO.WiggleIO(wigfhd).build_wigtrack()
wig_chr = wigtrack.get_data_by_chr(chrom)
if not wig_chr:
sys.stderr.write("No data for chromosome %s!\n" % chrom)
sys.exit(1)
newwigtrack = WigTrackI()
newwigtrack.span = wigtrack.span
(wig_chr_p, wig_chr_s) = wig_chr
for i in range(len(wig_chr_p)):
newwigtrack.add_loc(chrom, wig_chr_p[i], wig_chr_s[i])
newwigfile = sys.argv[3]
newwigfhd = open(newwigfile, "w")
newwigtrack.write_wig(newwigfhd, name="for chromosome %s" % chrom)
newwigfhd.close()
def main():
if len(sys.argv) < 4:
sys.stderr.write("Extract data for certain chromosome from a wiggle file.\n")
sys.stderr.write("need 3 paras: %s <chr> <wig> <newwig>\n" % os.path.basename(sys.argv[0]))
sys.exit(1)
chrom = sys.argv[1]
wigfhd = open(sys.argv[2])
wigtrack = WiggleIO.WiggleIO(wigfhd).build_wigtrack()
wig_chr = wigtrack.get_data_by_chr(chrom)
if not wig_chr:
sys.stderr.write("No data for chromosome %s!\n" % chrom)
sys.exit(1)
newwigtrack = WigTrackI()
newwigtrack.span = wigtrack.span
(wig_chr_p,wig_chr_s) = wig_chr
for i in range(len(wig_chr_p)):
newwigtrack.add_loc(chrom,wig_chr_p[i],wig_chr_s[i])
newwigfile = sys.argv[3]
newwigfhd = open(newwigfile,"w")
newwigtrack.write_wig(newwigfhd,name="for chromosome %s" % chrom)
newwigfhd.close()
def main():
if len(sys.argv) < 3:
sys.stderr.write(
"Extract data for all chromosomes from a wiggle file.\n")
sys.stderr.write("need 2 paras: %s <wig> <output_prefix>\n" %
os.path.basename(sys.argv[0]))
sys.exit(1)
wigfhd = open(sys.argv[1])
prefix = sys.argv[2]
wigtrack = WiggleIO.WiggleIO(wigfhd).build_wigtrack()
wigtrack.sort()
for chrom in wigtrack.get_chr_names():
wig_chr = wigtrack.get_data_by_chr(chrom)
newwigtrack = WigTrackI()
newwigtrack.span = wigtrack.span
(wig_chr_p, wig_chr_s) = wig_chr
for i in range(len(wig_chr_p)):
newwigtrack.add_loc(chrom, wig_chr_p[i], wig_chr_s[i])
newwigfile = sys.argv[2] + "." + chrom + ".wig"
newwigfhd = open(newwigfile, "w")
newwigtrack.write_wig(newwigfhd, name="for chromosome %s" % chrom)
newwigfhd.close()