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)