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
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'])
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'])