Ejemplo n.º 1
0
 def stats(self):
     result = {}
     result['raw'] = tail(self.p.out)
     # Special cases #
     if "by concatenation not pandaseq" in result['raw']:
         result['noalign'] = 0
         result['lowqual'] = 0
         result['loss']    = 0
         return result
     # Normal case #
     if "pandaseq: error" in result['raw']: raise Exception("Pandaseq did not run properly")
     if result['raw'].startswith("ERR\t"): raise Exception("Pandaseq did not run properly")
     result['distrib'] = re.findall('STAT\tOVERLAPS\t(.+)$', result['raw'], re.M)
     result['distrib'] = map(int, result['distrib'][0].split())
     result['lengths'] = flatter([[i+1]*v for i,v in enumerate(result['distrib'])])
     result['noalign'] = int(re.findall('STAT\tNOALGN\t(.+)$', result['raw'], re.M)[0])
     result['lowqual'] = int(re.findall('STAT\tLOWQ\t(.+)$', result['raw'], re.M)[0])
     result['loss'] = 100 * sum(result['distrib'][100:]) / sum(result['distrib'])
     return result
Ejemplo n.º 2
0
 def log_tail(self):
     """If we have a log file, what is its tail"""
     if not self.kwargs['out_file'].exists: return False
     else: return tail(self.slurm_params['out_file'])
Ejemplo n.º 3
0
 def log_tail(self):
     """If we have a log file, what is its tail"""
     if not self.kwargs['out_file'].exists: return False
     else: return tail(self.slurm_params['out_file'])