def __init__(self,work_path,compact,sample_name,lib_method,data_type):
self.work_times = 0 # rework times
self.result = {}
self.compact = compact
self.sample_name = sample_name
self.lib_method = lib_method
self.data_type = data_type
# get path
self.path = { 'QC' : '%s/QC'%work_path,
'split' : '%s/Split'%work_path,
}
self.path['compact'] = '%s/%s'%(self.path['QC'],self.compact)
self.path['sample'] = '%s/%s_%s'%(self.path['compact'],self.sample_name,lib_method)
try:
self.check_path()
except:
sys.stderr.write('## Permisson ERROR!\t#some problem accured when create path!\n')
return False
#get read
raw_reads_path = '%s/%s/%s'%(self.path['split'],self.compact,self.sample_name)
try:
(self.read1,self.read2) = get_reads(raw_reads_path,self.lib_method)
except:
sys.stderr.write('### row reads read failed! %s:%s\n'%(self.compact,self.sample_name))
return False
#get primer
self.f_primer,self.r_primer = get_primer(lib_method,data_type)
def __init__(self,work_path,compact,sample_name,lib_method,data_type):
self.work_times = 0 # rework times
self.result = {}
self.compact = compact
self.sample_name = sample_name
self.lib_method = lib_method
self.data_type = data_type
# get path
self.path = { 'QC' : '%s/QC'%work_path,
'split' : '%s/Split'%work_path,
}
self.path['compact'] = '%s/%s'%(self.path['QC'],self.compact)
self.path['sample'] = '%s/%s_%s'%(self.path['compact'],self.sample_name,lib_method)
try:
self.check_path()
except:
sys.stderr.write('## Permisson ERROR!\t#some problem accured when create path!\n')
#get read
raw_reads_path = '%s/%s/%s'%(self.path['split'],self.compact,self.sample_name)
try:
read1,read2 = get_reads(raw_reads_path,self.lib_method)
self.read = Reads(read1,read2)
except Exception,ex:
sys.stderr.write('%s:%s\n'%(Exception,ex))
def stat_raw_reads(self,compact,data_type,lib_method,sample_name):
raw_path = '%s/%s/%s'%(self.path['split'],compact,sample_name)
try:
(read_file,read_file2) = get_reads(raw_path,lib_method)
reads_num = self.get_fq_num(read_file)
self.sample_struct[compact][data_type][lib_method][sample_name]['raw_reads'] = reads_num
self.total_reads[lib_method] += reads_num
except:
sys.stderr.write('get raw data failed: %s:%s\n'%(compact,sample_name))
self.sample_struct[compact][data_type][lib_method][sample_name]['raw_reads'] = 0
