def prepare(self): # for quick testing, we recover parameters here ws_client = self.common_params['ws_client'] hs = self.common_params['hs_client'] params = self.method_params logger = self.logger token = self.common_params['user_token'] cuffdiff_dir = self.directory self.details = rnaseq_util.get_details_for_diff_exp( logger, ws_client, hs, params['ws_id'], self.urls, cuffdiff_dir, params['expressionset_id'], token) self.num_threads = mp.cpu_count() self.num_jobs = 1 als = [] for l in self.details['labels']: rep_files = ",".join([ os.path.join(cuffdiff_dir + '/' + l, sub + '/accepted_hits.bam') for sub in os.listdir(os.path.join(cuffdiff_dir, l)) if os.path.isdir(os.path.join(cuffdiff_dir, l + '/' + sub)) ]) als.append(rep_files) self.bam_files = " ".join([i for i in als]) self.t_labels = ",".join(self.details['labels']) self.task_list = [self.__class__]
def prepare(self): # for quick testing, we recover parameters here ws_client = self.common_params['ws_client'] hs = self.common_params['hs_client'] params = self.method_params logger = self.logger token = self.common_params['user_token'] cuffdiff_dir = self.directory self.details = rnaseq_util.get_details_for_diff_exp(logger,ws_client,hs,params['ws_id'],self.urls,cuffdiff_dir,params['expressionset_id'],token) self.num_threads = mp.cpu_count() self.num_jobs = 1 als = [] for l in self.details['labels']: rep_files=",".join([ os.path.join(cuffdiff_dir+'/'+l,sub+'/accepted_hits.bam') for sub in os.listdir(os.path.join(cuffdiff_dir,l)) if os.path.isdir(os.path.join(cuffdiff_dir,l+'/'+sub))]) als.append(rep_files) self.bam_files = " ".join([i for i in als]) self.t_labels = ",".join(self.details['labels']) self.task_list = [self.__class__]
def prepare(self): # for quick testing, we recover parameters here ws_client = self.common_params['ws_client'] hs = self.common_params['hs_client'] params = self.method_params logger = self.logger token = self.common_params['user_token'] diffexp_dir = self.directory self.details = rnaseq_util.get_details_for_diff_exp(logger,ws_client,hs,params['ws_id'],self.urls,diffexp_dir,params['expressionset_id'],token) self.num_threads = mp.cpu_count() self.num_jobs = 1 als = [] for l in self.details['labels']: rep_files=[ (os.path.join(diffexp_dir+'/'+l,sub+'/accepted_hits.bam'), os.path.join(diffexp_dir+'/'+l,sub+'/transcripts.gtf')) for sub in os.listdir(os.path.join(diffexp_dir,l)) if os.path.isdir(os.path.join(diffexp_dir,l+'/'+sub))] #rep_files=",".join([ os.path.join(diffexp_dir+'/'+l,sub+'/accepted_hits.bam') for sub in os.listdir(os.path.join(diffexp_dir,l)) if os.path.isdir(os.path.join(diffexp_dir,l+'/'+sub))]) als += rep_files ### Call Cuffmerge function used_tool = self.details['used_tool'] merge_dir = os.path.join(diffexp_dir,"merge") if used_tool == 'StringTie': run_tool = "StringTie" tool_version = "1.2.3" merged_gtf = rnaseq_util.call_stringtiemerge(diffexp_dir,merge_dir,self.num_threads,self.details['gtf_file'],self.details['gtf_list_file']) elif used_tool == 'Cufflinks': merged_gtf = rnaseq_util.call_cuffmerge(diffexp_dir,merge_dir,num_threads,gtf_file,self.details['gtf_list_file']) run_tool = "Tablemaker" tool_version = '2.0.9' merged_gtf = rnaseq_util.call_cuffmerge(diffexp_dir,merge_dir,self.num_threads,self.details['gtf_file'],self.details['gtf_list_file']) self.bam_files = " ".join([i for i in als]) self.t_labels = ",".join(self.details['labels']) ballgown_dir = os.path.join(diffexp_dir,"ballgown") if not os.path.exists(ballgown_dir): os.mkdir(ballgown_dir) ### Make Input_dir from expression_file_name self.task_list = [self.__class__]