for lanes_dictionary in gerald_object.eland_results.results:
for eland_lane in lanes_dictionary.values():
- source_name = eland_lane.pathname
- if source_name is None:
- LOGGER.info(
- "Lane ID %s does not have a filename." % (eland_lane.lane_id,))
- else:
- path, name = os.path.split(source_name)
- dest_name = os.path.join(cycle_dir, name)
- LOGGER.info("Saving eland file %s to %s" % \
- (source_name, dest_name))
-
- if is_compressed(name):
- LOGGER.info('Already compressed, Saving to %s' % (dest_name,))
- shutil.copy(source_name, dest_name)
- else:
- # not compressed
- dest_name += '.bz2'
- args = ['bzip2', '-9', '-c', source_name, '>', dest_name ]
- bz_commands.append(" ".join(args))
- #LOGGER.info('Running: %s' % ( " ".join(args) ))
- #bzip_dest = open(dest_name, 'w')
- #bzip = subprocess.Popen(args, stdout=bzip_dest)
- #LOGGER.info('Saving to %s' % (dest_name, ))
- #bzip.wait()
+ for source_name in eland_lane.pathnames:
+ if source_name is None:
+ LOGGER.info(
+ "Lane ID %s does not have a filename." % (eland_lane.lane_id,))
+ else:
+ path, name = os.path.split(source_name)
+ dest_name = os.path.join(cycle_dir, name)
+ LOGGER.info("Saving eland file %s to %s" % \
+ (source_name, dest_name))
+
+ if is_compressed(name):
+ LOGGER.info('Already compressed, Saving to %s' % (dest_name,))
+ shutil.copy(source_name, dest_name)
+ else:
+ # not compressed
+ dest_name += '.bz2'
+ args = ['bzip2', '-9', '-c', source_name, '>', dest_name ]
+ bz_commands.append(" ".join(args))
+ #LOGGER.info('Running: %s' % ( " ".join(args) ))
+ #bzip_dest = open(dest_name, 'w')
+ #bzip = subprocess.Popen(args, stdout=bzip_dest)
+ #LOGGER.info('Saving to %s' % (dest_name, ))
+ #bzip.wait()
if len(bz_commands) > 0:
q = QueueCommands(bz_commands, num_jobs)