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__]
