def write(queue_in, queue_out, filename, cpus):
from jcvi.utils.progressbar import ProgressBar, Percentage, Bar, ETA
fw = must_open(filename, "w")
isize = queue_in.qsize()
logging.debug("A total of {0} items to compute.".format(isize))
isize = isize or 1
widgets = [
'Queue: ',
Percentage(), ' ',
Bar(marker='>', left='[', right=']'), ' ',
ETA()
]
p = ProgressBar(maxval=isize, term_width=60, widgets=widgets).start()
poisons = 0
while True:
res = queue_out.get()
qsize = queue_in.qsize()
p.update(isize - qsize)
if isinstance(res, Poison):
poisons += 1
if poisons == cpus: # wait all workers finish
break
elif res:
print(res, file=fw)
fw.flush()
fw.close()
def write(queue_in, queue_out, filename, cpus):
from jcvi.utils.progressbar import ProgressBar, Percentage, Bar, ETA
fw = must_open(filename, "w")
isize = queue_in.qsize()
logging.debug("A total of {0} items to compute.".format(isize))
isize = isize or 1
widgets = ["Queue: ", Percentage(), " ", Bar(marker=">", left="[", right="]"), " ", ETA()]
p = ProgressBar(maxval=isize, term_width=60, widgets=widgets).start()
poisons = 0
while True:
res = queue_out.get()
qsize = queue_in.qsize()
p.update(isize - qsize)
if isinstance(res, Poison):
poisons += 1
if poisons == cpus: # wait all workers finish
break
elif res:
print >> fw, res
fw.flush()
fw.close()
def weblogo(args):
"""
%prog weblogo fastqfile
Extract base composition for reads
"""
import numpy as np
from jcvi.utils.progressbar import ProgressBar, Percentage, Bar, ETA
p = OptionParser(weblogo.__doc__)
p.add_option("-N", default=10, type="int",
help="Count the first and last N bases")
p.add_option("--nreads", default=1000000, type="int",
help="Parse first N reads")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastqfile, = args
N = opts.N
nreads = opts.nreads
pat = "ATCG"
L = np.zeros((4, N), dtype="int32")
R = np.zeros((4, N), dtype="int32")
p = dict((a, i) for (i, a) in enumerate(pat))
L4, R3 = Counter(), Counter()
widgets = ['Parse reads: ', Percentage(), ' ',
Bar(marker='>', left='[', right=']'), ' ', ETA()]
pr = ProgressBar(maxval=nreads, term_width=60, widgets=widgets).start()
k = 0
fw_L = open("L.fasta", "w")
fw_R = open("R.fasta", "w")
for rec in iter_fastq(fastqfile):
k += 1
if k % 1000 == 0:
pr.update(k)
if k > nreads:
break
if rec is None:
break
s = rec.seq
for i, a in enumerate(s[:N]):
a = p[a]
L[a][i] += 1
for j, a in enumerate(s[-N:][::-1]):
a = p[a]
R[a][N - 1 - j] += 1
l4, r3 = s[:4], s[-3:]
L4[l4] += 1
R3[r3] += 1
print >> fw_L, ">{0}\n{1}".format(k, s[:N])
print >> fw_R, ">{0}\n{1}".format(k, s[-N:])
fw_L.close()
fw_R.close()
cmd = "weblogo -F png -s large -f {0}.fasta -o {0}.png"
cmd += " --color-scheme classic --composition none -U probability"
cmd += " --title {1}"
sh(cmd.format('L', "First_10_bases"))
sh(cmd.format('R', "Last_10_bases"))
np.savetxt("L.{0}.csv".format(pat), L, delimiter=',', fmt="%d")
np.savetxt("R.{0}.csv".format(pat), R, delimiter=',', fmt="%d")
fw = open("L4.common", "w")
for p, c in L4.most_common(N):
print >> fw, "\t".join((p, str(c)))
fw.close()
fw = open("R3.common", "w")
for p, c in R3.most_common(N):
print >> fw, "\t".join((p, str(c)))
fw.close()
def weblogo(args):
"""
%prog weblogo [fastafile|fastqfile]
Extract base composition for reads
"""
import numpy as np
from jcvi.utils.progressbar import ProgressBar, Percentage, Bar, ETA
p = OptionParser(weblogo.__doc__)
p.add_option("-N", default=10, type="int",
help="Count the first and last N bases")
p.add_option("--nreads", default=1000000, type="int",
help="Parse first N reads")
opts, args = p.parse_args(args)
if len(args) != 1:
sys.exit(not p.print_help())
fastqfile, = args
N = opts.N
nreads = opts.nreads
pat = "ATCG"
L = np.zeros((4, N), dtype="int32")
R = np.zeros((4, N), dtype="int32")
p = dict((a, i) for (i, a) in enumerate(pat))
L4, R3 = Counter(), Counter()
widgets = ['Parse reads: ', Percentage(), ' ',
Bar(marker='>', left='[', right=']'), ' ', ETA()]
pr = ProgressBar(maxval=nreads, term_width=60, widgets=widgets).start()
k = 0
fw_L = open("L.fasta", "w")
fw_R = open("R.fasta", "w")
fastq = fastqfile.endswith(".fastq")
it = iter_fastq(fastqfile) if fastq else \
SeqIO.parse(must_open(fastqfile), "fasta")
for rec in it:
k += 1
if k % 1000 == 0:
pr.update(k)
if k > nreads:
break
if rec is None:
break
s = str(rec.seq)
for i, a in enumerate(s[:N]):
if a in p:
a = p[a]
L[a][i] += 1
for j, a in enumerate(s[-N:][::-1]):
if a in p:
a = p[a]
R[a][N - 1 - j] += 1
l4, r3 = s[:4], s[-3:]
L4[l4] += 1
R3[r3] += 1
print >> fw_L, ">{0}\n{1}".format(k, s[:N])
print >> fw_R, ">{0}\n{1}".format(k, s[-N:])
fw_L.close()
fw_R.close()
cmd = "weblogo -F png -s large -f {0}.fasta -o {0}.png"
cmd += " --color-scheme classic --composition none -U probability"
cmd += " --title {1}"
sh(cmd.format('L', "First_10_bases"))
sh(cmd.format('R', "Last_10_bases"))
np.savetxt("L.{0}.csv".format(pat), L, delimiter=',', fmt="%d")
np.savetxt("R.{0}.csv".format(pat), R, delimiter=',', fmt="%d")
fw = open("L4.common", "w")
for p, c in L4.most_common(N):
print >> fw, "\t".join((p, str(c)))
fw.close()
fw = open("R3.common", "w")
for p, c in R3.most_common(N):
print >> fw, "\t".join((p, str(c)))
fw.close()
