def s01_Trim(self):
sh_file = "%s/s01.Trim.sh" % (self.scripts)
sh_work_file = "%s/s01.Trim_work.sh" % (self.scripts)
l_sh_info = self.s_01_trim()
l_sh_work = []
for samp in self.samInfo_pd_RNA['sample']:
print samp
idx = (self.samInfo_pd_RNA['sample'] == samp)
brief_name = self.samInfo_pd_RNA[idx]['brief_name'].values[0]
make_dir([self.dir_trim_data, brief_name])
for i in os.walk('%s/%s' % (self.dir_raw_data, samp)):
in_fq1 = "%s/%s" % (i[0], i[2][0])
in_fq2 = "%s/%s" % (i[0], i[2][1])
if in_fq1.split('_')[-2] == "R2":
in_fq2 = "%s/%s" % (i[0], i[2][0])
in_fq1 = "%s/%s" % (i[0], i[2][1])
l_sh_work.append("sh %s %s %s %s" % \
(sh_file, in_fq1, in_fq2, brief_name)
)
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s02_Bismark(self):
sh_file = "%s/s02.Bismark.sh" % (self.scripts)
sh_work_file = "%s/s02.Bismark_work.sh" % (self.scripts)
l_sh_info = self.s_02_bismark()
l_sh_work = []
for brief_name in self.samInfo_pd_RNA['brief_name']:
print brief_name
idx = (self.samInfo_pd_RNA['brief_name'] == brief_name)
sample = self.samInfo_pd_RNA[idx]['sample'].values[0]
make_dir([self.dir_bismark, brief_name])
for i in os.walk('%s/%s' % (self.dir_raw_data, sample)):
in_fq1 = "%s_val_1.fq.gz" % (i[2][0].split(".")[0])
in_fq2 = "%s_val_2.fq.gz" % (i[2][1].split(".")[0])
if in_fq1.split('_')[-2] == "R2":
in_fq2 = "%s_val_2.fq.gz" % (i[2][0].split(".")[0])
in_fq1 = "%s_val_1.fq.gz" % (i[2][1].split(".")[0])
l_sh_work.append("sh %s %s %s %s %s" % \
(sh_file, brief_name, in_fq1, in_fq2, self.ref)
)
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=3, is_debug=self.is_debug)
def s08_plotDist(self):
sh_file = "%s/s08.plotDist.sh" % (self.scripts)
sh_work_file = "%s/s08.plotDist_work.sh" % (self.scripts)
l_sh_info = self.s_08_plotDist()
l_sh_work = []
fai_input = "%s/%s/%s_lambda.fa.fai" % (self.Database, self.ref,
self.ref)
for query in self.l_query:
mergeRatio = "%s/%s/%s/RatioMatrix.xls" % (self.dir_StatInfo,
self.s_idx, query)
db_file = "%s/%s/%s_lambda.fa.%s.anno.bed" % (
self.Database, self.ref, self.ref, query)
outprefix = "%s/%s/%s/plot" % (self.dir_StatInfo, self.s_idx,
query)
sam_file = "%s/%s.%s.allsamp.xls" % (self.dir_StatInfo, self.s_idx,
query)
l_sh_work.append(
"sh %s %s %s %s %s" %
(sh_file, mergeRatio, db_file, outprefix, sam_file))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s05_NDR(self, pvalue=15):
sh_file = "%s/s05.NDR.sh" % (self.scripts)
sh_work_file = "%s/s05.NDR_work.sh" % (self.scripts)
l_sh_info = self.s_05_NDR()
l_sh_work = []
fai_input = "%s/%s/%s_lambda.fa.fai" % (self.Database, self.ref,
self.ref)
self.l_chrom = []
f_fai_input = open(fai_input, "r")
for line in f_fai_input:
line = line.strip("\n")
f = line.split()
self.l_chrom.append(f[0])
f_fai_input.close()
self.__load_ChrInfo()
for brief_name in self.samInfo_pd_RNA['brief_name']:
for query in self.l_query:
for chrom in self.l_chrom:
l_sh_work.append(
"sh %s %s %s %s %d %d %d" %
(sh_file, brief_name, query, chrom,
self.M_QuerySamChr[query][brief_name]['all']['umt'],
self.M_QuerySamChr[query][brief_name]['all']['met'],
pvalue))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s03_Bam2SingleC(self):
sh_file = "%s/s03.Bam2SingleC.sh" % (self.scripts)
sh_work_file = "%s/s03.Bam2SingleC_work.sh" % (self.scripts)
l_sh_info = self.s_03_Bam2SingleC()
l_sh_work = []
fai_input = "%s/%s/%s_lambda.fa.fai" % (self.Database, self.ref,
self.ref)
self.l_chrom = []
f_fai_input = open(fai_input, "r")
for line in f_fai_input:
line = line.strip("\n")
f = line.split()
self.l_chrom.append(f[0])
f_fai_input.close()
for brief_name in self.samInfo_pd_RNA['brief_name']:
make_dir([self.dir_singleC, brief_name, "bam"])
make_dir([self.dir_singleC, brief_name, "singleC"])
for chrom in self.l_chrom:
l_sh_work.append("sh %s %s %s %s %s" %
(sh_file, brief_name, chrom, self.ref,
" ".join(self.l_query)))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s09_2_Het_long(self):
sh_file = "%s/s09.2.Het_long.sh" % (self.scripts)
sh_work_file = "%s/s09.2.Het_long_work.sh" % (self.scripts)
l_sh_info = self.s_09_2_HetLong_motif()
l_sh_work = []
for brief_name in self.samInfo_pd_RNA['brief_name']:
l_sh_work.append("sh %s %s" % (sh_file, brief_name))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s11_NDR_motif(self):
sh_file = "%s/s11.NDR_motif.sh" % (self.scripts)
sh_work_file = "%s/s11.NDR_motif_work.sh" % (self.scripts)
l_sh_info = self.s_11_NDR_motif()
l_sh_work = []
for brief_name in self.samInfo_pd_RNA['brief_name']:
l_sh_work.append("sh %s %s %s" % (sh_file, brief_name, self.ref))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s10_NDR_flanking(self):
sh_file = "%s/s10.NDR_flanking.sh" % (self.scripts)
sh_work_file = "%s/s10.NDR_flanking_work.sh" % (self.scripts)
l_sh_info = self.s_10_NDR_flanking()
l_sh_work = []
make_dir([self.dir_NDR_flanking])
make_dir([self.dir_NDR, "distal_region"])
make_dir([self.dir_NDR, "TSS_region"])
for brief_name in self.samInfo_pd_RNA['brief_name']:
l_sh_work.append("sh %s %s %s" % (sh_file, brief_name, self.ref))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s09_NDR_IGV(self):
sh_file = "%s/s09.NDR_IGV.sh" % (self.scripts)
sh_work_file = "%s/s09.NDR_IGV_work.sh" % (self.scripts)
l_sh_info = self.s_09_NDR_IGV()
l_sh_work = []
fai_input = "%s/%s/%s_lambda.fa.fai" % (self.Database, self.ref,
self.ref)
make_dir([self.dir_NDR])
for brief_name in self.samInfo_pd_RNA['brief_name']:
for query in self.l_query:
l_sh_work.append("sh %s %s %s %s" %
(sh_file, brief_name, query, self.ref))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s06_merge_singleC(self):
sh_file = "%s/s06.mergeSC.sh" % (self.scripts)
sh_work_file = "%s/s06.mergeSC_work.sh" % (self.scripts)
l_sh_info = self.s_06_mergeSC()
l_sh_work = []
fai_input = "%s/%s/%s_lambda.fa.fai" % (self.Database, self.ref,
self.ref)
for brief_name in self.samInfo_pd_RNA['brief_name']:
for query in self.l_query:
l_sh_work.append("sh %s %s %s %s" %
(sh_file, brief_name, query, self.ref))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
def s04_statMeth(self, depth=5):
sh_file = "%s/s04.StatLog.sh" % (self.scripts)
sh_work_file = "%s/s04.StatLog_work.sh" % (self.scripts)
l_sh_info = self.s_04_StatLog()
l_sh_work = []
fai_input = "%s/%s/%s_lambda.fa.fai" % (self.Database, self.ref,
self.ref)
for brief_name in self.samInfo_pd_RNA['brief_name']:
for query in self.l_query:
l_sh_work.append("sh %s %s %s %d %s" %
(sh_file, brief_name, self.ref, depth, query))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=8, is_debug=self.is_debug)
self.__load_ChrInfo()
print self.M_QuerySamChr
for query in self.l_query:
outfile = "%s/%s.%s.allsamp.xls" % (self.dir_StatInfo, self.s_idx,
query)
f_outfile = open(outfile, "w")
print >> f_outfile, "sample\tall_umt\tall_met\tall_cnt\tlambda_umt\tlambda_met\tlambda_cnt"
for brief_name in self.samInfo_pd_RNA['brief_name']:
print >> f_outfile, "%s\t%d\t%d\t%d\t%d\t%d\t%d" % (
brief_name,
self.M_QuerySamChr[query][brief_name]['all']['umt'],
self.M_QuerySamChr[query][brief_name]['all']['met'],
self.M_QuerySamChr[query][brief_name]['all']['cnt'],
self.M_QuerySamChr[query][brief_name]['lambda']['umt'],
self.M_QuerySamChr[query][brief_name]['lambda']['met'],
self.M_QuerySamChr[query][brief_name]['lambda']['cnt'])
f_outfile.close()