def __init__(self,illumina_run_dir):
"""Create and populate a new IlluminaRun object
Arguments:
illumina_run_dir: path to the top-level directory holding
the 'raw' sequencing data
"""
# Top-level directory
self.run_dir = os.path.abspath(illumina_run_dir)
# Platform
self.platform = platforms.get_sequencer_platform(self.run_dir)
if self.platform is None:
raise Exception("Can't determine platform for %s" % self.run_dir)
elif self.platform not in ('illumina-ga2x','hiseq','miseq'):
raise Exception("%s: not an Illumina sequencer?" % self.run_dir)
# Basecalls subdirectory
self.basecalls_dir = os.path.join(self.run_dir,
'Data','Intensities','BaseCalls')
if os.path.isdir(self.basecalls_dir):
# Locate sample sheet
self.sample_sheet_csv = os.path.join(self.basecalls_dir,'SampleSheet.csv')
if not os.path.isfile(self.sample_sheet_csv):
self.sample_sheet_csv = None
else:
self.basecalls_dir = None
# RunInfo.xml
self.runinfo_xml = os.path.join(self.run_dir,'RunInfo.xml')
if not os.path.isfile(self.runinfo_xml):
self.runinfo_xml = None
def __init__(self, illumina_run_dir):
"""Create and populate a new IlluminaRun object
Arguments:
illumina_run_dir: path to the top-level directory holding
the 'raw' sequencing data
"""
# Top-level directory
self.run_dir = os.path.abspath(illumina_run_dir)
# Platform
self.platform = platforms.get_sequencer_platform(self.run_dir)
if self.platform is None:
raise Exception("Can't determine platform for %s" % self.run_dir)
elif self.platform not in ('illumina-ga2x', 'hiseq', 'miseq'):
raise Exception("%s: not an Illumina sequencer?" % self.run_dir)
# Basecalls subdirectory
self.basecalls_dir = os.path.join(self.run_dir, 'Data', 'Intensities',
'BaseCalls')
if os.path.isdir(self.basecalls_dir):
# Locate sample sheet
self.sample_sheet_csv = os.path.join(self.basecalls_dir,
'SampleSheet.csv')
if not os.path.isfile(self.sample_sheet_csv):
self.sample_sheet_csv = None
else:
self.basecalls_dir = None
# RunInfo.xml
self.runinfo_xml = os.path.join(self.run_dir, 'RunInfo.xml')
if not os.path.isfile(self.runinfo_xml):
self.runinfo_xml = None
'--no-log',
action='store_true',
dest="no_log",
default=False,
help="write rsync output directly stdout, don't create a log file")
options, args = p.parse_args()
if len(args) != 2:
p.error("input is a source directory and a destination")
# Locate source directory (and strip any trailing slash)
data_dir = os.path.abspath(args[0].rstrip(os.sep))
if not os.path.isdir(data_dir):
logging.error("%s: doesn't exist or is not a directory" % data_dir)
sys.exit(1)
# Determine platform
if options.platform is None:
platform = platforms.get_sequencer_platform(data_dir)
if platform is None:
logging.error("Can't determine platform: use --platform option?")
sys.exit(1)
else:
platform = options.platform
# Work out the destination
if options.year is None:
year = time.strftime("%Y")
else:
year = options.year
destination = os.path.join(args[1], year, platform)
# Log file
if not options.no_log:
log_file = "rsync.%s.log" % os.path.split(data_dir)[-1]
else:
help="mirror the source directory at the destination (update files "
"that have changed and remove any that have been deleted i.e. "
"rsync --delete-after)")
p.add_option('--no-log',action='store_true',dest="no_log",default=False,
help="write rsync output directly stdout, don't create a log file")
options,args = p.parse_args()
if len(args) != 2:
p.error("input is a source directory and a destination")
# Locate source directory (and strip any trailing slash)
data_dir = os.path.abspath(args[0].rstrip(os.sep))
if not os.path.isdir(data_dir):
logging.error("%s: doesn't exist or is not a directory" % data_dir)
sys.exit(1)
# Determine platform
if options.platform is None:
platform = platforms.get_sequencer_platform(data_dir)
if platform is None:
logging.error("Can't determine platform: use --platform option?")
sys.exit(1)
else:
platform = options.platform
# Work out the destination
if options.year is None:
year = time.strftime("%Y")
else:
year = options.year
destination = os.path.join(args[1],year,platform)
# Log file
if not options.no_log:
log_file = "rsync.%s.log" % os.path.split(data_dir)[-1]
else: