def __init__(self, *args, **kwargs):
"""
"""
BasicOrf.__init__(self, *args, **kwargs)
# list for tcode scores on certain positions
self._tcode_score_list = [None] * self.length
# list for tcode scores on certain positions
# status options are
# None no score for this position)
# -1 Non-coding
# 0 No opinion
# 1 Coding
self._tcode_status_list = [None] * self.length
self._tcode2status = {'Non-coding': -1, 'No opinion': 0, 'Coding': 1}
self._tcode_stats = ()
self._RAW_TCODE_DATA = []
def __init__(self,*args,**kwargs):
"""
"""
BasicOrf.__init__(self,*args,**kwargs)
# list for tcode scores on certain positions
self._tcode_score_list = [None]*self.length
# list for tcode scores on certain positions
# status options are
# None no score for this position)
# -1 Non-coding
# 0 No opinion
# 1 Coding
self._tcode_status_list = [None]*self.length
self._tcode2status = { 'Non-coding': -1, 'No opinion': 0, 'Coding': 1 }
self._tcode_stats = ()
self._RAW_TCODE_DATA = []
def __init__(self,*args,**kwargs):
"""
"""
BasicOrf.__init__(self,*args,**kwargs)
# data attributes for splice sites and TSS on this orf
self._donor_sites = []
self._acceptor_sites = []
self._has_donor_sites_predicted = False
self._has_acceptor_sites_predicted = False
self._projected_donor_sites = []
self._projected_acceptor_sites = []
self._tss_sites = []
self._has_tss_predicted = False
self._signalp_sites = []
self._has_signalp_sites_predicted = False
# attributes that hold the settings with which
# pssm sites are searched for
self.TSS_MIN_PSSM_SCORE = None
self.MIN_ACCEPTOR_PSSM_SCORE = None
self.MIN_DONOR_PSSM_SCORE = None
def __init__(self, *args, **kwargs):
"""
"""
BasicOrf.__init__(self, *args, **kwargs)
TcodeOrf.__init__(self, *args, **kwargs)
CodingOrf.__init__(self, *args, **kwargs)
def __init__(self,*args,**kwargs):
"""
"""
BasicOrf.__init__(self,*args,**kwargs)
TcodeOrf.__init__(self,*args,**kwargs)
CodingOrf.__init__(self,*args,**kwargs)
