def __init__(self,start,phase=None,strand=None,gff={}):
# initialize object from parental SliceSiteBase class
SpliceSiteBase.__init__(self,start,phase=phase,strand=strand,pattern=None,
pattern_offset=(0,0),pssm_score=None,gff=gff)
self.end = self.start+2
self.pos = self.start
self.donor = "GT"
def __init__(self,start,pattern,donor="GT",phase=None,strand=None,
pattern_offset=IC_DONOR_PATTERN_OFFSET,pssm_score=None,gff={}):
# initialize object from parental SliceSiteBase class
SpliceSiteBase.__init__(self,start,phase=phase,strand=strand,gff=gff,
pattern=pattern,pattern_offset=pattern_offset,pssm_score=pssm_score)
self.end = self.start + 2 + self._offset_5p + self._offset_3p
self.pos = self.start + self._offset_5p
self.donor = donor.upper()
def __init__(self,start,pattern,acceptor="AG",phase=None,strand=None,
pattern_offset=IC_ACCEPTOR_PATTERN_OFFSET,pssm_score=None,gff={}):
# initialize object from parental SliceSiteBase class
SpliceSiteBase.__init__(self,start,phase=phase,strand=strand,gff=gff,
pattern=pattern,pattern_offset=pattern_offset,pssm_score=pssm_score)
self.end = self.start + 2 + self._offset_5p + self._offset_3p
self.pos = self.end - self._offset_3p
self.acceptor = acceptor
def __init__(self, start, phase=None, strand=None, gff={}):
# initialize object from parental SliceSiteBase class
SpliceSiteBase.__init__(self,
start,
phase=phase,
strand=strand,
pattern=None,
pattern_offset=(0, 0),
pssm_score=None,
gff=gff)
self.end = self.start + 2
self.pos = self.end
self.acceptor = "AG"
def togff(self, gff={}):
"""
Overrides SpliceSiteBase.togff()
Takes care for proper fstart and fstop setting
"""
self._gff['fstart'] = self.pos - 1
self._gff['fstop'] = self.pos
return SpliceSiteBase.togff(self, gff=gff)
def togff(self,gff={}):
"""
Overrides SpliceSiteBase.togff()
Takes care for proper fstart and fstop setting
"""
self._gff['fstart'] = self.pos-1
self._gff['fstop'] = self.pos
return SpliceSiteBase.togff(self,gff=gff)
def __init__(self,
start,
pattern,
acceptor="AG",
phase=None,
strand=None,
pattern_offset=IC_ACCEPTOR_PATTERN_OFFSET,
pssm_score=None,
gff={}):
# initialize object from parental SliceSiteBase class
SpliceSiteBase.__init__(self,
start,
phase=phase,
strand=strand,
gff=gff,
pattern=pattern,
pattern_offset=pattern_offset,
pssm_score=pssm_score)
self.end = self.start + 2 + self._offset_5p + self._offset_3p
self.pos = self.end - self._offset_3p
self.acceptor = acceptor
def __init__(self,
start,
pattern,
donor="GT",
phase=None,
strand=None,
pattern_offset=IC_DONOR_PATTERN_OFFSET,
pssm_score=None,
gff={}):
# initialize object from parental SliceSiteBase class
SpliceSiteBase.__init__(self,
start,
phase=phase,
strand=strand,
gff=gff,
pattern=pattern,
pattern_offset=pattern_offset,
pssm_score=pssm_score)
self.end = self.start + 2 + self._offset_5p + self._offset_3p
self.pos = self.start + self._offset_5p
self.donor = donor.upper()
def togff(self, gff={}):
"""
Overrides SpliceSiteBase.togff()
Takes care for proper fstart and fstop setting
"""
self._gff['fstart'] = self.pos + 1
self._gff['fstop'] = self.pos + 2
if not self.is_canonical():
if not self._gff.has_key('column9data'):
self._gff['column9data'] = {}
self._gff['column9data']['Non-canonical'] = self.donor
# return basal pliceSiteBase.togff() function
return SpliceSiteBase.togff(self, gff=gff)
def togff(self,gff={}):
"""
Overrides SpliceSiteBase.togff()
Takes care for proper fstart and fstop setting
"""
self._gff['fstart'] = self.pos+1
self._gff['fstop'] = self.pos+2
if not self.is_canonical():
if not self._gff.has_key('column9data'):
self._gff['column9data'] = {}
self._gff['column9data']['Non-canonical'] = self.donor
# return basal pliceSiteBase.togff() function
return SpliceSiteBase.togff(self,gff=gff)
