def merge_RPKM_uniq( self ):
m01.make_dir([ self.dir_RPM_mrg ])
sh_file = "%s/s15.MergeRPKM.sh" % (self.scripts)
sh_work_file = "%s/s15.1.MergeRPKM_work.sh" % (self.scripts)
l_brief = self.samInfo_pd_ChIP['brief_name']
l_merge = set(self.samInfo_pd_ChIP['merge_name'])
l_sh_info = self.s15_merge_RPKM()
l_sh_work = []
for window in [ "100","1kb" ]:
for ltype in ["rep","mrg"]:
l_sam = l_brief
RPKM_dir = self.dir_RPM_bins_rep
if ltype == "mrg":
l_sam = l_merge
RPKM_dir = self.dir_RPM_bins_mrg
header = "\"#chr\\tbeg\\tend\\t%s\"" % ("\\t".join(l_sam))
l_RPKM_file = [
"%s/%s/%s.RPKM.uniq.%s" %\
(RPKM_dir,sam,sam,window) for sam in l_sam
]
l_sh_work.append(
"sh %s %s %s %s %s" %\
(sh_file, header, window, ltype, " ".join(l_RPKM_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 run_macs_rep(self, pvalue=0.001, ref="hs", core_num=4):
sh_file = "%s/s06.1.macs2PeakRep.sh" % (self.scripts)
sh_work_file = "%s/s06.1.macs2PeakRep_work.sh" % (self.scripts)
l_sh_info = self.s06_1_macs2PeakRep(ref)
l_sh_work = []
for brief_name in self.samInfo_pd_ChIP['brief_name']:
idx = (self.samInfo_pd_ChIP['brief_name'] == brief_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_rep, brief_name])
ctrl_name = self.samInfo_pd_ChIP[idx]['control'].values[0]
shift_size = 300
f_shiftSize = "%s/%s/out/out.tab" %\
(self.dir_spp_rep_shiftSize, brief_name )
if os.path.isfile(f_shiftSize):
val = get_shiftSize(f_shiftSize)
if val > 0:
shift_size = val
l_sh_work.append("sh %s %s %s %f %d" %\
(sh_file, brief_name, ctrl_name, pvalue, shift_size))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=core_num, is_debug=self.is_debug)
def run_anno_peak(self,
TSS_genebody_up,
TSS_genebody_down,
TSS_promoter_up,
TSS_promoter_down,
ext_binlen=50,
body_bincnt=100,
tss_binlen=1):
sh_file = "%s/s12.PeakGeneRegion.sh" % (self.scripts)
sh_work_file = "%s/s12.PeakGeneRegion_work.sh" % (self.scripts)
l_sh_info = self.s12_PeakGeneRegion(TSS_genebody_up,
TSS_genebody_down,
TSS_promoter_up,
TSS_promoter_down,
ext_binlen=50,
body_bincnt=100,
tss_binlen=1)
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
m01.make_dir([self.dir_Peak_mrg_TSS, merge_name])
m01.make_dir([self.dir_Peak_mrg_Gene, merge_name])
l_sh_work.append("sh %s %s" % (sh_file, merge_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 merge_RPKM_uniq(self):
m01.make_dir([self.dir_RPM_mrg])
sh_file = "%s/s15.MergeRPKM.sh" % (self.scripts)
sh_work_file = "%s/s15.1.MergeRPKM_work.sh" % (self.scripts)
l_brief = self.samInfo_pd_ChIP['brief_name']
l_merge = set(self.samInfo_pd_ChIP['merge_name'])
l_sh_info = self.s15_merge_RPKM()
l_sh_work = []
for window in ["100", "1kb"]:
for ltype in ["rep", "mrg"]:
l_sam = l_brief
RPKM_dir = self.dir_RPM_bins_rep
if ltype == "mrg":
l_sam = l_merge
RPKM_dir = self.dir_RPM_bins_mrg
header = "\"#chr\\tbeg\\tend\\t%s\"" % ("\\t".join(l_sam))
l_RPKM_file = [
"%s/%s/%s.RPKM.uniq.%s" %\
(RPKM_dir,sam,sam,window) for sam in l_sam
]
l_sh_work.append(
"sh %s %s %s %s %s" %\
(sh_file, header, window, ltype, " ".join(l_RPKM_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 make_igv_broad(self):
sh_file = "%s/s11.makeIGV_broad.sh" %\
(self.scripts)
sh_work_repPeak_file = "%s/s11.3.makeIGV.repBroadPeak_work.sh" %\
(self.scripts)
sh_work_mrgPeak_file = "%s/s11.4.makeIGV.mrgBroadPeak_work.sh" %\
(self.scripts)
l_sh_info = self.s11_makeIGV_broad()
l_sh_work_rep = []
l_sh_work_mrg = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_BroadPeak_TDF, merge_name])
l_brief = list(self.samInfo_pd_ChIP[idx]['brief_name'])
for brief in l_brief:
l_sh_work_rep.append("sh %s %s %s %s" %\
(sh_file, brief, merge_name, self.dir_BroadPeak_rep))
l_sh_work_mrg.append("sh %s %s %s %s" %\
(sh_file, merge_name, merge_name, self.dir_BroadPeak_mrg))
my_job_rep = m_jobs.run_jobs(sh_file, sh_work_repPeak_file, \
l_sh_info, l_sh_work_rep)
my_job_mrg = m_jobs.run_jobs(sh_file, sh_work_mrgPeak_file, \
l_sh_info, l_sh_work_mrg)
my_job_rep.running_multi(cpu=8, is_debug=self.is_debug)
my_job_mrg.running_multi(cpu=8, is_debug=self.is_debug)
def make_igv_broad(self, core_num=4):
sh_file = "%s/s11.makeIGV_broad.sh" %\
(self.scripts)
sh_work_repPeak_file = "%s/s11.3.makeIGV.repBroadPeak_work.sh" %\
(self.scripts)
sh_work_mrgPeak_file = "%s/s11.4.makeIGV.mrgBroadPeak_work.sh" %\
(self.scripts)
l_sh_info = self.s11_makeIGV_broad()
l_sh_work_rep = []
l_sh_work_mrg = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_BroadPeak_TDF, merge_name])
l_brief = list(self.samInfo_pd_ChIP[idx]['brief_name'])
for brief in l_brief:
l_sh_work_rep.append("sh %s %s %s %s" %\
(sh_file, brief, merge_name, self.dir_BroadPeak_rep))
l_sh_work_mrg.append("sh %s %s %s %s" %\
(sh_file, merge_name, merge_name, self.dir_BroadPeak_mrg))
my_job_rep = m_jobs.run_jobs(sh_file, sh_work_repPeak_file, \
l_sh_info, l_sh_work_rep)
my_job_mrg = m_jobs.run_jobs(sh_file, sh_work_mrgPeak_file, \
l_sh_info, l_sh_work_mrg)
my_job_rep.running_multi(cpu=core_num, is_debug=self.is_debug)
my_job_mrg.running_multi(cpu=core_num, is_debug=self.is_debug)
def run_macs_rep( self, pvalue=0.001, ref="hs" ):
sh_file = "%s/s06.1.macs2PeakRep.sh" % (self.scripts)
sh_work_file = "%s/s06.1.macs2PeakRep_work.sh" % (self.scripts)
l_sh_info = self.s06_1_macs2PeakRep( ref )
l_sh_work = []
for brief_name in self.samInfo_pd_ChIP['brief_name']:
idx =(self.samInfo_pd_ChIP['brief_name'] == brief_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_rep, brief_name])
ctrl_name = self.samInfo_pd_ChIP[ idx ]['control'].values[0]
shift_size = 300
f_shiftSize = "%s/%s/out/out.tab" %\
(self.dir_spp_rep_shiftSize, brief_name )
if os.path.isfile( f_shiftSize ):
val = get_shiftSize( f_shiftSize )
if val > 0:
shift_size = val
l_sh_work.append("sh %s %s %s %f %d" %\
(sh_file, brief_name, ctrl_name, pvalue, shift_size))
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 merge_density_100bp(self, core_num=4):
m01.make_dir([self.dir_RPM_mrg])
sh_file = "%s/s17.MergeDensity.sh" % (self.scripts)
sh_work_file = "%s/s17.MergeDensity_work.sh" % (self.scripts)
l_brief = self.samInfo_pd_ChIP['brief_name']
l_merge = set(self.samInfo_pd_ChIP['merge_name'])
l_brief2 = []
for brief_name in l_brief:
idx = (self.samInfo_pd_ChIP['brief_name'] == brief_name)
if self.__is_input(idx):
continue
l_brief2.append(brief_name)
l_merge2 = []
for merge_name in l_merge:
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
l_merge2.append(merge_name)
l_brief = l_brief2
l_merge = l_merge2
l_sh_info = self.s17_merge_RPKM()
l_sh_work = []
for ltype in ["rep", "mrg"]:
l_sam = l_brief
RPKM_dir = self.dir_Peak_rep
if ltype == "mrg":
l_sam = l_merge
RPKM_dir = self.dir_Peak_mrg
header = "\"#chr\\tbeg\\tend\\t%s\"" % ("\\t".join(l_sam))
l_RPKM_file = [
"%s/%s/%s.1kb.norm_avg.xls" %\
(RPKM_dir, sam, sam) for sam in l_sam
]
l_sh_work.append(
"sh %s %s %s %s %s" %\
(sh_file, header, "1kb", ltype, " ".join(l_RPKM_file))
)
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=core_num, is_debug=self.is_debug)
def merge_density_100bp(self):
m01.make_dir([ self.dir_RPM_mrg ])
sh_file = "%s/s17.MergeDensity.sh" % (self.scripts)
sh_work_file = "%s/s17.MergeDensity_work.sh" % (self.scripts)
l_brief = self.samInfo_pd_ChIP['brief_name']
l_merge = set(self.samInfo_pd_ChIP['merge_name'])
l_brief2 = []
for brief_name in l_brief:
idx =(self.samInfo_pd_ChIP['brief_name'] == brief_name)
if self.__is_input(idx):
continue
l_brief2.append(brief_name)
l_merge2 = []
for merge_name in l_merge:
idx =(self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
l_merge2.append(merge_name)
l_brief = l_brief2
l_merge = l_merge2
l_sh_info = self.s17_merge_RPKM()
l_sh_work = []
for ltype in ["rep","mrg"]:
l_sam = l_brief
RPKM_dir = self.dir_Peak_rep
if ltype == "mrg":
l_sam = l_merge
RPKM_dir = self.dir_Peak_mrg
header = "\"#chr\\tbeg\\tend\\t%s\"" % ("\\t".join(l_sam))
l_RPKM_file = [
"%s/%s/%s.1kb.norm_avg.xls" %\
(RPKM_dir, sam, sam) for sam in l_sam
]
l_sh_work.append(
"sh %s %s %s %s %s" %\
(sh_file, header, "1kb", ltype, " ".join(l_RPKM_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 div_bed_to_bins_unique_mrg(self):
sh_file = "%s/s14.RPM_density_rep.sh" % (self.scripts)
sh_work_file = "%s/s14.RPM_density_rep_work.sh" % (self.scripts)
l_sh_info = self.s14_RPM_density_mrg()
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
m01.make_dir([ self.dir_RPM_bins_mrg, merge_name])
mapped_reads = np.sum(self.stat_Info.StatInfo[merge_name]['q30'])
l_sh_work.append("sh %s %s %d" % (sh_file,merge_name, mapped_reads))
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 div_bed_to_bins_unique_mrg(self):
sh_file = "%s/s14.RPM_density_rep.sh" % (self.scripts)
sh_work_file = "%s/s14.RPM_density_rep_work.sh" % (self.scripts)
l_sh_info = self.s14_RPM_density_mrg()
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
m01.make_dir([self.dir_RPM_bins_mrg, merge_name])
mapped_reads = np.sum(self.stat_Info.StatInfo[merge_name]['q30'])
l_sh_work.append("sh %s %s %d" %
(sh_file, merge_name, mapped_reads))
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 get_shift_size_mrg(self):
sh_file = "%s/s05.2.spp_mrg_shiftSize.sh" % (self.scripts)
sh_work_file = "%s/s05.2.spp_mrg_shiftSize_work.sh" % (self.scripts)
l_sh_info = self.s05_2_spp_mrg_shiftSize()
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx =(self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_spp_mrg_shiftSize, merge_name, "test"])
m01.make_dir([self.dir_spp_mrg_shiftSize, merge_name, "out" ])
l_sh_work.append("sh %s %s" % ( sh_file, merge_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 get_shift_size_mrg(self, core_num=4):
sh_file = "%s/s05.2.spp_mrg_shiftSize.sh" % (self.scripts)
sh_work_file = "%s/s05.2.spp_mrg_shiftSize_work.sh" % (self.scripts)
l_sh_info = self.s05_2_spp_mrg_shiftSize()
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_spp_mrg_shiftSize, merge_name, "test"])
m01.make_dir([self.dir_spp_mrg_shiftSize, merge_name, "out"])
l_sh_work.append("sh %s %s" % (sh_file, merge_name))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=core_num, is_debug=self.is_debug)
def run_macs_rep_broad(self, pvalue=0.05, ref="hs"):
sh_file = "%s/s08.macs2BroadPeakRep.sh" % (self.scripts)
sh_work_file = "%s/s08.macs2BroadPeakRep_work.sh" % (self.scripts)
l_sh_info = self.s08_macs2BroadPeakRep( ref )
l_sh_work = []
for brief_name in self.samInfo_pd_ChIP['brief_name']:
idx =(self.samInfo_pd_ChIP['brief_name'] == brief_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_BroadPeak_rep, brief_name])
ctrl_name = self.samInfo_pd_ChIP[idx]['control'].values[0]
l_sh_work.append("sh %s %s %s %f" %\
( sh_file, brief_name, ctrl_name, 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 div_bed_to_bins_unique_rep(self):
sh_file = "%s/s13.RPM_density_rep.sh" % (self.scripts)
sh_work_file = "%s/s13.RPM_density_rep_work.sh" % (self.scripts)
l_sh_info = self.s13_RPM_density_rep()
l_sh_work = []
for brief_name in self.samInfo_pd_ChIP['brief_name']:
m01.make_dir([ self.dir_RPM_bins_rep, brief_name])
idx = (self.samInfo_pd_ChIP['brief_name'] == brief_name)
merge_name = self.samInfo_pd_ChIP[ idx ]['merge_name'].values[0]
l_brief = self.stat_Info.StatInfo[merge_name]['l_brief']
idx2 = l_brief.index(brief_name)
mapped_reads = self.stat_Info.StatInfo[merge_name]['q30'][idx2]
l_sh_work.append("sh %s %s %d" % (sh_file, brief_name, mapped_reads))
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 prepare_idr_input(self, top_peak=100000, core_num=4):
sh_file = "%s/s07.1.IDR_prepare.sh" % (self.scripts)
sh_work_file = "%s/s07.1.IDR_prepare_work.sh" % (self.scripts)
l_sh_info = self.s07_1_IDR_prepare()
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_idr, merge_name])
l_brief = list(self.samInfo_pd_ChIP[idx]['brief_name'])
list_brief = " ".join(l_brief)
l_sh_work.append("sh %s %s %d %s" %
(sh_file, merge_name, top_peak, list_brief))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=core_num, is_debug=self.is_debug)
def run_macs_rep_broad(self, pvalue=0.05, ref="hs", core_num=4):
sh_file = "%s/s08.macs2BroadPeakRep.sh" % (self.scripts)
sh_work_file = "%s/s08.macs2BroadPeakRep_work.sh" % (self.scripts)
l_sh_info = self.s08_macs2BroadPeakRep(ref)
l_sh_work = []
for brief_name in self.samInfo_pd_ChIP['brief_name']:
idx = (self.samInfo_pd_ChIP['brief_name'] == brief_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_BroadPeak_rep, brief_name])
ctrl_name = self.samInfo_pd_ChIP[idx]['control'].values[0]
l_sh_work.append("sh %s %s %s %f" %\
( sh_file, brief_name, ctrl_name, pvalue ))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=core_num, is_debug=self.is_debug)
def div_bed_to_bins_unique_rep(self):
sh_file = "%s/s13.RPM_density_rep.sh" % (self.scripts)
sh_work_file = "%s/s13.RPM_density_rep_work.sh" % (self.scripts)
l_sh_info = self.s13_RPM_density_rep()
l_sh_work = []
for brief_name in self.samInfo_pd_ChIP['brief_name']:
m01.make_dir([self.dir_RPM_bins_rep, brief_name])
idx = (self.samInfo_pd_ChIP['brief_name'] == brief_name)
merge_name = self.samInfo_pd_ChIP[idx]['merge_name'].values[0]
l_brief = self.stat_Info.StatInfo[merge_name]['l_brief']
idx2 = l_brief.index(brief_name)
mapped_reads = self.stat_Info.StatInfo[merge_name]['q30'][idx2]
l_sh_work.append("sh %s %s %d" %
(sh_file, brief_name, mapped_reads))
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 run_macs_mrg_broad(self, pvalue=0.05, ref="hs"):
sh_file = "%s/s09.macs2BroadPeakMrg.sh" % (self.scripts)
sh_work_file = "%s/s09.macs2BroadPeakMrg_work.sh" % (self.scripts)
l_sh_info = self.s09_macs2BroadPeakMrg(ref)
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_mrg, merge_name])
ctrl_name = self.samInfo_pd_ChIP[idx]['control'].values[0]
l_sh_work.append("sh %s %s %s %f" % \
(sh_file, merge_name, ctrl_name, 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 prepare_idr_input(self, top_peak = 100000):
sh_file = "%s/s07.1.IDR_prepare.sh" % (self.scripts)
sh_work_file = "%s/s07.1.IDR_prepare_work.sh" % (self.scripts)
l_sh_info = self.s07_1_IDR_prepare()
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx =(self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir( [ self.dir_Peak_idr, merge_name ] )
l_brief = list(self.samInfo_pd_ChIP[ idx ]['brief_name'])
list_brief = " ".join(l_brief)
l_sh_work.append(
"sh %s %s %d %s" % (sh_file, merge_name, top_peak,list_brief)
)
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 run_macs_mrg_broad(self, pvalue=0.05, ref="hs", core_num=4):
sh_file = "%s/s09.macs2BroadPeakMrg.sh" % (self.scripts)
sh_work_file = "%s/s09.macs2BroadPeakMrg_work.sh" % (self.scripts)
l_sh_info = self.s09_macs2BroadPeakMrg(ref)
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_mrg, merge_name])
ctrl_name = self.samInfo_pd_ChIP[idx]['control'].values[0]
l_sh_work.append("sh %s %s %s %f" % \
(sh_file, merge_name, ctrl_name, pvalue))
my_job = m_jobs.run_jobs(sh_file, sh_work_file, l_sh_info, l_sh_work)
my_job.running_multi(cpu=core_num, is_debug=self.is_debug)
def run_anno_peak(self,
TSS_genebody_up,TSS_genebody_down,TSS_promoter_up,
TSS_promoter_down,ext_binlen=50,body_bincnt=100,
tss_binlen=1):
sh_file = "%s/s12.PeakGeneRegion.sh" % (self.scripts)
sh_work_file = "%s/s12.PeakGeneRegion_work.sh" % (self.scripts)
l_sh_info = self.s12_PeakGeneRegion(
TSS_genebody_up,TSS_genebody_down,TSS_promoter_up,
TSS_promoter_down,ext_binlen=50,body_bincnt=100,
tss_binlen=1)
l_sh_work = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
m01.make_dir([ self.dir_Peak_mrg_TSS, merge_name ])
m01.make_dir([ self.dir_Peak_mrg_Gene, merge_name ])
l_sh_work.append("sh %s %s" % ( sh_file, merge_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 run_idr(self):
sh_file = \
"%s/s07.2.IDR_usingMacs2Peak.sh" % (self.scripts)
sh_work_file_rep = \
"%s/s07.2.IDR_usingMacs2Peak_rep_work.sh" % (self.scripts)
sh_work_file_self = \
"%s/s07.2.IDR_usingMacs2Peak_selfReps_work.sh" % (self.scripts)
sh_work_file_pool = \
"%s/s07.2.IDR_usingMacs2Peak_poolReps_work.sh" % (self.scripts)
l_sh_info = self.s07_2_usingMacs2Peak()
l_sh_work_rep = []
l_sh_work_self = []
l_sh_work_pool = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx =(self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_idr, merge_name])
l_brief = list(self.samInfo_pd_ChIP[idx]['brief_name'])
# print merge_name,l_brief,list(l_brief)
### IDR ANALYSIS ON ORIGINAL REPLICATES
subtype = "rep"
m01.make_dir([self.dir_Peak_idr, merge_name, subtype])
if len(l_brief) > 1:
for i in range( 0,len(l_brief)-1 ):
for j in range( i+1,len(l_brief) ):
in_sam1 = "%s" % (l_brief[i])
in_sam2 = "%s" % (l_brief[j])
l_sh_work_rep.append("sh %s %s %s %s %s" %\
(sh_file,in_sam1,in_sam2,merge_name,subtype))
### IDR ANALYSIS ON SELF-PSEUDOREPLICATES
subtype = "selfPseudoReps"
m01.make_dir([self.dir_Peak_idr, merge_name, subtype])
for sam in l_brief:
in_sam1 = "%s.pr1" % (sam)
in_sam2 = "%s.pr2" % (sam)
l_sh_work_self.append("sh %s %s %s %s %s" %\
(sh_file, in_sam1, in_sam2, merge_name, subtype))
### IDR ANALYSIS ON POOLED-PSEUDOREPLICATES
subtype = "pooledPseudoReps"
m01.make_dir([ self.dir_Peak_idr, merge_name, subtype ])
in_sam1 = "%s.pr1" % (merge_name)
in_sam2 = "%s.pr2" % (merge_name)
l_sh_work_pool.append("sh %s %s %s %s %s" %\
(sh_file, in_sam1, in_sam2, merge_name, subtype))
my_job_rep = m_jobs.run_jobs( \
sh_file, sh_work_file_rep, l_sh_info, l_sh_work_rep)
my_job_self = m_jobs.run_jobs( \
sh_file, sh_work_file_self, l_sh_info, l_sh_work_self)
my_job_pool = m_jobs.run_jobs( \
sh_file, sh_work_file_pool, l_sh_info, l_sh_work_pool)
my_job_rep.running_multi(cpu=8, is_debug=self.is_debug)
my_job_self.running_multi(cpu=8,is_debug=self.is_debug)
my_job_pool.running_multi(cpu=8,is_debug=self.is_debug)
def run_idr(self, core_num=4):
sh_file = \
"%s/s07.2.IDR_usingMacs2Peak.sh" % (self.scripts)
sh_work_file_rep = \
"%s/s07.2.IDR_usingMacs2Peak_rep_work.sh" % (self.scripts)
sh_work_file_self = \
"%s/s07.2.IDR_usingMacs2Peak_selfReps_work.sh" % (self.scripts)
sh_work_file_pool = \
"%s/s07.2.IDR_usingMacs2Peak_poolReps_work.sh" % (self.scripts)
l_sh_info = self.s07_2_usingMacs2Peak()
l_sh_work_rep = []
l_sh_work_self = []
l_sh_work_pool = []
for merge_name in set(self.samInfo_pd_ChIP['merge_name']):
idx = (self.samInfo_pd_ChIP['merge_name'] == merge_name)
if self.__is_input(idx):
continue
m01.make_dir([self.dir_Peak_idr, merge_name])
l_brief = list(self.samInfo_pd_ChIP[idx]['brief_name'])
# print merge_name,l_brief,list(l_brief)
### IDR ANALYSIS ON ORIGINAL REPLICATES
subtype = "rep"
m01.make_dir([self.dir_Peak_idr, merge_name, subtype])
if len(l_brief) > 1:
for i in range(0, len(l_brief) - 1):
for j in range(i + 1, len(l_brief)):
in_sam1 = "%s" % (l_brief[i])
in_sam2 = "%s" % (l_brief[j])
l_sh_work_rep.append("sh %s %s %s %s %s" %\
(sh_file,in_sam1,in_sam2,merge_name,subtype))
### IDR ANALYSIS ON SELF-PSEUDOREPLICATES
subtype = "selfPseudoReps"
m01.make_dir([self.dir_Peak_idr, merge_name, subtype])
for sam in l_brief:
in_sam1 = "%s.pr1" % (sam)
in_sam2 = "%s.pr2" % (sam)
l_sh_work_self.append("sh %s %s %s %s %s" %\
(sh_file, in_sam1, in_sam2, merge_name, subtype))
### IDR ANALYSIS ON POOLED-PSEUDOREPLICATES
subtype = "pooledPseudoReps"
m01.make_dir([self.dir_Peak_idr, merge_name, subtype])
in_sam1 = "%s.pr1" % (merge_name)
in_sam2 = "%s.pr2" % (merge_name)
l_sh_work_pool.append("sh %s %s %s %s %s" %\
(sh_file, in_sam1, in_sam2, merge_name, subtype))
my_job_rep = m_jobs.run_jobs( \
sh_file, sh_work_file_rep, l_sh_info, l_sh_work_rep)
my_job_self = m_jobs.run_jobs( \
sh_file, sh_work_file_self, l_sh_info, l_sh_work_self)
my_job_pool = m_jobs.run_jobs( \
sh_file, sh_work_file_pool, l_sh_info, l_sh_work_pool)
my_job_rep.running_multi(cpu=core_num, is_debug=self.is_debug)
my_job_self.running_multi(cpu=core_num, is_debug=self.is_debug)
my_job_pool.running_multi(cpu=core_num, is_debug=self.is_debug)
