b = Bustard(bustard_pathname)
gerald_glob = os.path.join(bustard_pathname, 'GERALD*')
for gerald_pathname in glob(gerald_glob):
- g = GERALD(gerald_pathname)
- runs.append(PipelineRun(runfolder, f, b, g))
+ try:
+ g = GERALD(gerald_pathname)
+ runs.append(PipelineRun(runfolder, f, b, g))
+ except IOError, e:
+ print "Ignoring", str(e)
return runs
"""
for run in runs:
# print a run name?
- logging.info('Summarizing ' + run.name)
+ print 'Summary for', run.name
for lane in run.gerald.summary.lane_results:
print 'lane', lane.lane, 'clusters', lane.cluster[0], '+/-',
print lane.cluster[1]