def Step9_bedAnalysis(self):
jobs_tool = bedAnalysis(bedAnalysis_path=os.path.join(Rhea_Chip_Home, "tools", "cnv", "bedAnalysis.py"))
s_out = os.path.join(self.script, "Step9.bedAnalysis.sh")
bash = BASH("bedAnalysis", s_out, self.log)
cd = jobs_tool.analysis(region=self.region, reference=self.reference, rmsk=self.rmsk,
outdir=self.outdir, depthfile=",".join(self.SamplesDepth.values()))
cd = bash.stat_command_formact(cd, "bed region analysis")
bash.write(bash.bash_header_and_foot(cd, 'CNV bed region analysis'))
bash.close()
def Step9_bedAnalysis(self):
jobs_tool = bedAnalysis(bedAnalysis_path=os.path.join(
Rhea_Chip_Home, "tools", "cnv", "bedAnalysis.py"))
s_out = os.path.join(self.script, "Step9.bedAnalysis.sh")
bash = BASH("bedAnalysis", s_out, self.log)
cd = jobs_tool.analysis(region=self.region,
reference=self.reference,
rmsk=self.rmsk,
outdir=self.outdir,
depthfile=",".join(self.SamplesDepth.values()))
cd = bash.stat_command_formact(cd, "bed region analysis")
bash.write(bash.bash_header_and_foot(cd, 'CNV bed region analysis'))
bash.close()
def Step12_CNVCall(self):
jobs_tool = batCNV(batCNV_path=os.path.join(Rhea_Chip_Home, "tools", "cnv", "batCNV.py"))
for sample in self.samples:
s_out = os.path.join(self.script, "Step12.CNVCall.%s.sh" % sample)
bash = BASH("%s.CNVCall" % sample, s_out, self.log)
cd = jobs_tool.analysis(indir=self.outdir, dbdir=self.databases, sample=sample, correct_win_len=self.winlen,
correct_shift_len=self.siftlen, reference=self.reference, plot=self.plot)
cd = bash.stat_command_formact(cd, "%s CNV calling" % sample)
bash.write(bash.bash_header_and_foot(cd, '%s CNV calling' % sample))
bash.close()
def Step11_WinCorrect(self):
jobs_tool = WinCorrect(WinCorrect_path=os.path.join(Rhea_Chip_Home, "tools", "cnv", "WinCorrect.py"))
for chrom in self.contigs:
s_out = os.path.join(self.script, "Step11.WinCorrect.%s.sh" % chrom)
bash = BASH("%s.WinCorrect" % chrom, s_out, self.log)
cd = jobs_tool.analysis(region=self.region, chromstat=os.path.join(self.outdir, "chrom.stat"), chrom=chrom,
indir=self.outdir, correct_win_len=self.winlen, correct_shift_len=self.siftlen)
cd = bash.stat_command_formact(cd, "%s windows analysis and Correct" % chrom)
bash.write(bash.bash_header_and_foot(cd, '%s windows analysis and Correct' % chrom))
bash.close()
def Step12_CNVCall(self):
jobs_tool = batCNV(batCNV_path=os.path.join(Rhea_Chip_Home, "tools",
"cnv", "batCNV.py"))
for sample in self.samples:
s_out = os.path.join(self.script, "Step12.CNVCall.%s.sh" % sample)
bash = BASH("%s.CNVCall" % sample, s_out, self.log)
cd = jobs_tool.analysis(indir=self.outdir,
dbdir=self.databases,
sample=sample,
correct_win_len=self.winlen,
correct_shift_len=self.siftlen,
reference=self.reference,
plot=self.plot)
cd = bash.stat_command_formact(cd, "%s CNV calling" % sample)
bash.write(bash.bash_header_and_foot(cd,
'%s CNV calling' % sample))
bash.close()
def Step10_GCcorrect(self):
jobs_tool = GCcorrect(GCcorrect_path=os.path.join(Rhea_Chip_Home, "tools", "cnv", "GCcorrect.py"))
wingc = os.path.join(self.outdir, "win.gc")
posgc = os.path.join(self.outdir, "pos.gc")
chromstat = os.path.join(self.outdir, "chrom.stat")
for sample in self.samples:
cd = jobs_tool.correct(sample=sample, input=self.SamplesDepth[sample],
outdir=self.outdir, wingc=wingc,
posgc=posgc, chromstat=chromstat)
s_out = os.path.join(self.script, "Step10.GCcorrect.%s.sh" % sample)
bash = BASH("%s.GCcorrect" % sample, s_out, self.log)
cd = bash.stat_command_formact(cd, "Sample depth correct with GC")
bash.write(bash.bash_header_and_foot(cd, 'Sample depth correct with GC'))
bash.close()
def Step10_GCcorrect(self):
jobs_tool = GCcorrect(GCcorrect_path=os.path.join(
Rhea_Chip_Home, "tools", "cnv", "GCcorrect.py"))
wingc = os.path.join(self.outdir, "win.gc")
posgc = os.path.join(self.outdir, "pos.gc")
chromstat = os.path.join(self.outdir, "chrom.stat")
for sample in self.samples:
cd = jobs_tool.correct(sample=sample,
input=self.SamplesDepth[sample],
outdir=self.outdir,
wingc=wingc,
posgc=posgc,
chromstat=chromstat)
s_out = os.path.join(self.script,
"Step10.GCcorrect.%s.sh" % sample)
bash = BASH("%s.GCcorrect" % sample, s_out, self.log)
cd = bash.stat_command_formact(cd, "Sample depth correct with GC")
bash.write(
bash.bash_header_and_foot(cd, 'Sample depth correct with GC'))
bash.close()
def Step11_WinCorrect(self):
jobs_tool = WinCorrect(WinCorrect_path=os.path.join(
Rhea_Chip_Home, "tools", "cnv", "WinCorrect.py"))
for chrom in self.contigs:
s_out = os.path.join(self.script,
"Step11.WinCorrect.%s.sh" % chrom)
bash = BASH("%s.WinCorrect" % chrom, s_out, self.log)
cd = jobs_tool.analysis(region=self.region,
chromstat=os.path.join(
self.outdir, "chrom.stat"),
chrom=chrom,
indir=self.outdir,
correct_win_len=self.winlen,
correct_shift_len=self.siftlen)
cd = bash.stat_command_formact(
cd, "%s windows analysis and Correct" % chrom)
bash.write(
bash.bash_header_and_foot(
cd, '%s windows analysis and Correct' % chrom))
bash.close()
