def correct(args):
"""
%prog correct *.fastq
Correct reads using ErrorCorrection. Only PE will be used to build the K-mer
table.
"""
p = OptionParser(correct.__doc__)
p.add_cpus()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
lstfile = "reads2cor.lst"
fw = open(lstfile, "w")
print >> fw, "\n".join(x for x in args if x[:2] == "PE")
fw.close()
p1 = args[0]
offset = guessoffset([p1])
cpus = opts.cpus
freq = "output.freq.cz"
freqlen = freq + ".len"
if need_update(args, (freq, freqlen)):
cmd = "KmerFreq_AR_v2.0 -k 17 -c -1 -q {0}".format(offset)
cmd += " -m 1 -t {0}".format(cpus)
cmd += " -p output {0}".format(lstfile)
sh(cmd)
fw = open(lstfile, "w")
print >> fw, "\n".join(args)
fw.close()
cmd = "Corrector_AR_v2.0 -k 17 -l 3 -m 5 -c 5 -a 0 -e 1 -w 0 -r 45"
cmd += " -Q {0} -q 30 -x 8 -t {1} -o 1 ".format(offset, cpus)
cmd += " {0} {1} {2}".format(freq, freqlen, lstfile)
sh(cmd)
def correct(args):
"""
%prog correct *.fastq
Correct reads using ErrorCorrection. Only PE will be used to build the K-mer
table.
"""
p = OptionParser(correct.__doc__)
p.add_cpus()
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
lstfile = "reads2cor.lst"
fw = open(lstfile, "w")
print >> fw, "\n".join(x for x in args if x[:2] == "PE")
fw.close()
p1 = args[0]
offset = guessoffset([p1])
cpus = opts.cpus
freq = "output.freq.cz"
freqlen = freq + ".len"
if need_update(args, (freq, freqlen)):
cmd = "KmerFreq_AR_v2.0 -k 17 -c -1 -q {0}".format(offset)
cmd += " -m 1 -t {0}".format(cpus)
cmd += " -p output {0}".format(lstfile)
sh(cmd)
fw = open(lstfile, "w")
print >> fw, "\n".join(args)
fw.close()
cmd = "Corrector_AR_v2.0 -k 17 -l 3 -m 5 -c 5 -a 0 -e 1 -w 0 -r 45"
cmd += " -Q {0} -q 30 -x 8 -t {1} -o 1 ".format(offset, cpus)
cmd += " {0} {1} {2}".format(freq, freqlen, lstfile)
sh(cmd)
