def s04_novo_3_HTSeq_unknown(self): sh_file = "%s/s04.novo_3.HTSeq_unknown.sh" % self.scripts sh_work_file = "%s/s04.novo_3.HTSeq_unknown_work.sh" % self.scripts l_sh_info = self.s_04_3_novo_HTSeq_unknown() l_sh_work = [] dir_db = "%s/%s" % (self.Database, self.ref) unknown_GTF = "%s/novo_lnc_raw_%s.combined.gtf" % (dir_db, self.s_idx) for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([self.dir_HTS_unknown, brief_name]) l_sh_work.append("sh %s %s %s" % (sh_file, brief_name, unknown_GTF)) 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) # my_job.running_SGE(vf="400m", maxjob=100, is_debug = self.is_debug) m_01.make_dir([self.dir_HTS_result]) Gtf_Info = m_gtf.GTFFeature(unknown_GTF) Gtf_Info.gene_intergenic(self.intragenic_bed) Cnt_Info = m_cnt.CountInfo(self.dir_HTS_unknown, self.samInfo_pd_RNA['brief_name'], "dexseq_NeoRaw", self.dir_HTS_result) Cnt_Info.generate_mat() Cnt_Info.load_mat() Cnt_Info.cal_RPKM(Gtf_Info.gene, self.dir_tophat) rpkm_file = "%s/merge.%s.RPKM.xls" % (self.dir_HTS_result, "dexseq_NeoRaw") Gtf_Info.load_gene_RPKM(rpkm_file) Gtf_Info.output_GTF() Gtf_Info.get_gene_info()
def s03_HTSeq_known(self): sh_file = "%s/s03.HTSeq.sh" % (self.scripts) sh_work_file = "%s/s03.HTSeq_work.sh" % (self.scripts) l_sh_info = self.s_03_HTSeq_known() l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([self.dir_HTS_known, 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 s08_repeatCount(self): sh_file = "%s/s08.RepCnt.sh" % (self.scripts) sh_work_file = "%s/s08.RepCnt_work.sh" % (self.scripts) l_sh_info = self.s_08_repeatCount() l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([self.dir_repeat_counts, 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 s08_repeatCount(self): sh_file = "%s/s08.RepCnt.sh" % (self.scripts) sh_work_file = "%s/s08.RepCnt_work.sh" % (self.scripts) l_sh_info = self.s_08_repeatCount() l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([ self.dir_repeat_counts, 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 s03_HTSeq_known(self): sh_file = "%s/s03.HTSeq.sh" % (self.scripts) sh_work_file = "%s/s03.HTSeq_work.sh" % (self.scripts) l_sh_info = self.s_03_HTSeq_known() l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([ self.dir_HTS_known, 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 s06_1_cufflinks(self, cflk_dir, use_gtf): sh_file = "%s/s06.1.cflk.sh" % (self.scripts) sh_work_file = "%s/s06.1.cflk_work.sh" % (self.scripts) l_sh_info = self.s_06_1_cflk(cflk_dir) l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([cflk_dir, brief_name]) l_sh_work.append("sh %s %s %s" % (sh_file, brief_name, use_gtf)) 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_1_cufflinks(self, cflk_dir, use_gtf): sh_file = "%s/s06.1.cflk.sh" % (self.scripts) sh_work_file = "%s/s06.1.cflk_work.sh" % (self.scripts) l_sh_info = self.s_06_1_cflk(cflk_dir) l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([ cflk_dir, brief_name ]) l_sh_work.append("sh %s %s %s" % (sh_file, brief_name, use_gtf)) 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_novo_1_cufflinks_u(self): sh_file = "%s/s04.novo_1.cufflinks_unknown.sh" %\ (self.scripts) sh_work_file = "%s/s04.novo_1.cufflinks_unknown_work.sh" %\ (self.scripts) l_sh_info = self.s_04_1_novo_HTSeq_unknown() l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([self.dir_cufflinks_unknown, 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 s04_novo_1_cufflinks_u(self): sh_file = "%s/s04.novo_1.cufflinks_unknown.sh" %\ (self.scripts) sh_work_file = "%s/s04.novo_1.cufflinks_unknown_work.sh" %\ (self.scripts) l_sh_info = self.s_04_1_novo_HTSeq_unknown() l_sh_work = [] for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([ self.dir_cufflinks_unknown, 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 s07_cuffnorm(self, cflk_dir, cfnm_dir, use_gtf): sh_file = "%s/s07.cfnm.sh" % (self.scripts) sh_work_file = "%s/s07.cfnm_work.sh" % (self.scripts) l_sh_info = self.s_07_cfnm(cfnm_dir) l_sh_work = [] m_01.make_dir([cfnm_dir]) l_brief = self.samInfo_pd_RNA['brief_name'] l_cxb = ["%s/%s/abundances.cxb" % (cflk_dir, sam) for sam in l_brief] list_sam = ",".join(l_brief) list_cxb = " ".join(l_cxb) l_sh_work.append("sh %s %s %s %s" % (sh_file, list_sam, use_gtf, list_cxb)) 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 s07_cuffnorm(self, cflk_dir, cfnm_dir, use_gtf): sh_file = "%s/s07.cfnm.sh" % (self.scripts) sh_work_file = "%s/s07.cfnm_work.sh" % (self.scripts) l_sh_info = self.s_07_cfnm(cfnm_dir) l_sh_work = [] m_01.make_dir([ cfnm_dir ]) l_brief = self.samInfo_pd_RNA['brief_name'] l_cxb = [ "%s/%s/abundances.cxb" % (cflk_dir, sam) for sam in l_brief] list_sam = ",".join(l_brief) list_cxb = " ".join(l_cxb) l_sh_work.append( "sh %s %s %s %s" % (sh_file, list_sam, use_gtf, list_cxb) ) 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_novo_3_HTSeq_unknown(self): sh_file = "%s/s04.novo_3.HTSeq_unknown.sh" % self.scripts sh_work_file = "%s/s04.novo_3.HTSeq_unknown_work.sh" % self.scripts l_sh_info = self.s_04_3_novo_HTSeq_unknown() l_sh_work = [] dir_db = "%s/%s" % (self.Database, self.ref) unknown_GTF = "%s/novo_lnc_raw_%s.combined.gtf" % (dir_db, self.s_idx) for brief_name in self.samInfo_pd_RNA['brief_name']: m_01.make_dir([ self.dir_HTS_unknown, brief_name ]) l_sh_work.append("sh %s %s %s" %(sh_file, brief_name,unknown_GTF)) 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) # my_job.running_SGE(vf="400m", maxjob=100, is_debug = self.is_debug) m_01.make_dir([ self.dir_HTS_result ]) Gtf_Info = m_gtf.GTFFeature( unknown_GTF ) Gtf_Info.gene_intergenic( self.intragenic_bed ) Cnt_Info = m_cnt.CountInfo( self.dir_HTS_unknown, self.samInfo_pd_RNA['brief_name'], "dexseq_NeoRaw", self.dir_HTS_result ) Cnt_Info.generate_mat() Cnt_Info.load_mat() Cnt_Info.cal_RPKM(Gtf_Info.gene, self.dir_tophat) rpkm_file = "%s/merge.%s.RPKM.xls" % ( self.dir_HTS_result, "dexseq_NeoRaw" ) Gtf_Info.load_gene_RPKM( rpkm_file ) Gtf_Info.output_GTF() Gtf_Info.get_gene_info()