def clsCommandlineInterfaceArgv(argv=['clscli']):
commandline=' '.join(argv)
executablename = os.path.basename(argv[0])
argv.pop(0) # remove first argument (executable name), because we are explicitly passing it to parse_args
parser = argparse.ArgumentParser(description='CATHODE-CLI (Chronological Life Span Analysis Tool for '+
'High-throughput Optical Density Experiments): '+
'A commandline interface for extracting the chronological life span '+
'from multiple time series of optical density measurements.')
parser.add_argument('--version', action='store_true', default=None, help='show version and exit')
parser.add_argument('infiles', metavar='', nargs='*',
help='CATHODE file (.cat) or multiple GATHODE files (.gat)')
parser.add_argument('--day', metavar='float', action='append', type=float, dest='days',
help='day of lag/growthrate measurement of the corresponding plate file')
parser.add_argument('--viabilities', action='store', default=None, help='write viabilities to csv file')
parser.add_argument('--siplots', action='store', default=None, help='write survival intergal figures to pdf')
parser.add_argument('--labels', action='store', default=None, help='a file containing sampleid -> label and condition -> label mappings')
args = parser.parse_args(argv)
if args.version:
print(executablename+' '+__version__)
return 0
if len(args.infiles) == 0:
parser.print_help()
print('\ninput file(s) missing')
return -1
elif args.infiles[0].endswith(".cat"):
cls=Cls(serialisedFilename=args.infiles[0])
else:
cls=Cls(args.infiles,args.days)
if args.viabilities:
cls.survivalToCsv(args.viabilities)
if args.siplots:
labels={}
if args.labels is not None:
jsonfile=open(args.labels, 'r')
labels = json.loads(jsonfile.read())
jsonfile.close()
survivalIntegralsToPdf(cls,pdfout=args.siplots,
sampleIdToLabel=labels['sampleIdToLabel'] if 'sampleIdToLabel' in labels else None,
conditionToLabel=labels['conditionToLabel'] if 'conditionToLabel' in labels else None)
return 0
