obitools3/scripts/obi

#!/usr/local/bin/python3.5
'''
obi -- OBITools3

obi is a package for the management of analyses and data in DNA metabarcoding

@author:     Celine Mercier

@license:    CeCILL-V2

@contact:    celine.mercier@metabarcoding.org
'''


default_config = { 'software'       : "The OBITools 3",
                   'log'            : False,
                   'loglevel'       : 'INFO',
                   'inputURI'       : None,
                   'outputURI'      : None,
                   'defaultdms'     : None,
                   'inputview'      : None,
                   'outputview'     : None,
                   'skip'           : 0,
                   'only'           : None,
                   'fileformat'     : None,
                   'skiperror'      : True,
                   'qualityformat'  : b'sanger',
                   'offset'         : -1,
                   'noquality'      : False,
                   'seqtype'        : b'nuc',
                   "header"         : False,
                   "sep"            : None,
                   "quote"          : [b"'",b'"'],
                   "dec"            : b".",
                   "nastring"       : b"NA",
                   "stripwhite"     : True,
                   "blanklineskip"  : True,
                   "commentchar"    : b"#",
                   "nocreatedms"    : False
                  }

root_config_name='obi'

from obitools3.apps.config import getConfiguration     # @UnresolvedImport
from obitools3.version import version

__all__     = []
__version__ = version
__date__    = '2019-09-22'
__updated__ = '2019-09-22'

DEBUG = 1
TESTRUN = 0
PROFILE = 0


if __name__ =="__main__":
    
    config = getConfiguration(root_config_name,
                              default_config)    
                
    config[root_config_name]['module'].run(config)