Commit b9792f29 authored by Gerald Salin's avatar Gerald Salin
Browse files

add logging

parent 5c006f81
......@@ -96,21 +96,12 @@ class Run(object):
Copy, archive and compress the files list to the run. And add info to the run
@param mode: can be none, gz, bz2, tar.gz and tar.bz2
"""
# nb_seq, full_size = 0, 0
# for file in self.raw_files:
# try:
# # Get nb_seq and full_size values
# reader = seqio.SequenceReader(file)
# for id, desc, seq, qualities in reader:
# nb_seq += 1
# full_size += len(seq)
# except:
# logging.getLogger("Run.sync").debug(file + " seems to not be a seq file")
logging.getLogger("Run").debug("process_raw_files. set_full_size()")
self.set_nb_sequences(total_seq)
self.set_full_size(total_size)
# if not os.path.isdir(self.__get_work_directory()) :
# os.makedirs(self.__get_work_directory(), 0o751)
# self.archive_files(self.raw_files, mode)
logging.getLogger("Run").debug("process_raw_files. set_full_size("+str(total_size) + ")")
logging.getLogger("Run").debug("process_raw_files. set_nb_sequences("+str(total_seq) + ")")
def archive_files(self, files, mode, archive_name="ng6_archive.tar", delete=False):
......
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