def main():
p = optparse.OptionParser(__doc__)
p.add_option("-D", "--debug", action="store_true", dest="D", help="debug")
p.add_option("-N", "--novel", action="store_true", dest="novel",\
help="Only check at novel loci")
options, args = p.parse_args()
fh = csv.reader(open(args[0], "rU"), delimiter="\t")
debug = 0
unanno = re.compile(r"^RP[0-9]")
for line in fh:
if line[11] == "yes" and (line[1] =="-" or unanno.match(line[1])):
region, start, end = regionParse(line[2])
print("\t".join([region, str(start-1), str(end), line[0], line[1]]))
if options.D:
debug += 1
if debug > 10:
break
def main():
import optparse
p = optparse.OptionParser(__doc__)
p.add_option("-D", "--debug", action="store_true", dest="D", help="debug")
p.add_option("-S",
"--stam",
action="store_true",
dest="S",
help="DNAseI\
is generated from STAM's group")
p.add_option("-s",
"--shift",
action="store",
dest="shift",
help="Amount to\
shift the negative strand",
default=36)
ro.conversion.py2ri = numpy2ri
options, args = p.parse_args()
options.shift = int(options.shift)
bamfile = pysam.Samfile(args[0], 'rb')
region_str = regionParse(args[1])
chrom = region_str[0]
start = region_str[1]
end = region_str[2]
diff = end - start
a = np.zeros(2 * (diff), dtype=np.int)
try:
for alignment in bamfile.fetch(chrom, start, end):
if alignment.pos - start < 0: pass
else:
if alignment.is_reverse:
try:
a[alignment.pos - start + diff + options.shift] += 1
except IndexError:
pass
else:
a[alignment.pos - start] += 1
except ValueError:
pass
#########################################
# R plotting set-up
#########################################
r = ro.r
graphics = importr('graphics')
grdevices = importr('grDevices')
grdevices.png(file="/home/hsuj/projects/dnaseq/Stam/test.png",
width=1000,
height=1000)
"""
base = importr('base')
datasets = importr('datasets')
mtcars = datasets.mtcars
pp = ggplot2.ggplot(mtcars) + \
ggplot2.aes_string(x='wt', y='mpg', col='factor(cyl)') + \
ggplot2.geom_point() + \
ggplot2.geom_smooth(ggplot2.aes_string(group='cyl'),
method='lm')
pp.plot()
"""
graphics.plot(a[1:diff], main="test", pch=19, cex=0.5)
graphics.points(a[diff + 1:2 * diff], col="red", pch=19, cex=0.5)
grdevices.dev_off()
x = np.arange(1, diff, 1)
data2 = savitzky_golay(a, 9, 2)
plt.plot(x, data2[1:diff], 'b-', x, data2[diff + 1:2 * diff], 'r-')
plt.show()
def main():
import optparse
p = optparse.OptionParser(__doc__)
p.add_option("-D", "--debug", action="store_true", dest="D", help="debug")
p.add_option("-S", "--stam", action="store_true", dest="S", help="DNAseI\
is generated from STAM's group")
p.add_option("-s", "--shift", action="store", dest="shift", help="Amount to\
shift the negative strand", default = 36)
ro.conversion.py2ri = numpy2ri
options, args = p.parse_args()
options.shift = int(options.shift)
bamfile = pysam.Samfile(args[0], 'rb')
region_str = regionParse(args[1])
chrom = region_str[0]
start = region_str[1]
end = region_str[2]
diff = end-start
a = np.zeros(2*(diff), dtype=np.int)
try:
for alignment in bamfile.fetch(chrom, start, end):
if alignment.pos-start < 0: pass
else:
if alignment.is_reverse:
try:
a[alignment.pos-start+diff+options.shift] += 1
except IndexError:
pass
else:
a[alignment.pos-start] += 1
except ValueError:
pass
#########################################
# R plotting set-up
#########################################
r = ro.r
graphics = importr('graphics')
grdevices = importr('grDevices')
grdevices.png(file="/home/hsuj/projects/dnaseq/Stam/test.png", width=1000,
height=1000)
"""
base = importr('base')
datasets = importr('datasets')
mtcars = datasets.mtcars
pp = ggplot2.ggplot(mtcars) + \
ggplot2.aes_string(x='wt', y='mpg', col='factor(cyl)') + \
ggplot2.geom_point() + \
ggplot2.geom_smooth(ggplot2.aes_string(group='cyl'),
method='lm')
pp.plot()
"""
graphics.plot(a[1:diff], main="test", pch=19, cex=0.5)
graphics.points(a[diff+1:2*diff], col="red", pch=19, cex=0.5)
grdevices.dev_off()
x = np.arange(1, diff, 1)
data2 =savitzky_golay(a, 9, 2)
plt.plot(x, data2[1:diff], 'b-',x, data2[diff+1:2*diff], 'r-')
plt.show()
def fetchSeq(diff_line, bamFile):
region = regionParse(diff_line[2])
seq_call = Seq_call()
bamFile.fetch(region[0], region[1], region[2], callback=seq_call)
return(seq_call.sequences)
