def togff(self, gff={}):
""" Overwrites BasicGFF.togff() functionality """
if not self._gff.has_key('gname'):
self._gff['gname'] = "%s_%s" % (self.start, self.end)
if not self._gff.has_key('gclass'):
self._gff['gclass'] = self.__class__.__name__
# call basal BasicGFF.togff() function
gfflines = [BasicGFF.togff(self)]
# gff default for TSS/ATG
tss_gff = {
'fref': self._gff['fref'],
'gname': self._gff['gname'],
'gclass': self._gff['gclass'],
}
# if SignalPeptide is spliced -> make 2 tracks!
if self.intron:
# calculate lengths
signalp_length = self.end - self.start
signalp_5p_length = self.intron.donor.pos - self.start
signalp_3p_length = signalp_length - signalp_5p_length
# create SignalP 5p and 3p tracks
exon5p = list(gfflines[0])
exon3p = list(gfflines[0])
exon5p[4] = self.intron.donor.pos
exon3p[3] = self.intron.acceptor.pos + 1
exon3p[4] = self.intron.acceptor.pos + signalp_3p_length
if self.tss: exon5p[3] += 3
gfflines = [tuple(exon5p), tuple(exon3p)]
if self.tss: gfflines.insert(0, self.tss.togff(gff=tss_gff))
elif self.tss:
# correct SignalPeptide start coord to 1nt after the ATG codon
track = list(gfflines[0])
track[3] += 3
gfflines = [tuple(track)]
gfflines.insert(0, self.tss.togff(gff=tss_gff))
else:
pass
# return list with gff tuples
return gfflines
def togff(self,gff={}):
""" Overwrites BasicGFF.togff() functionality """
if not self._gff.has_key('gname'):
self._gff['gname'] = "%s_%s" % (self.start,self.end)
if not self._gff.has_key('gclass'):
self._gff['gclass'] = self.__class__.__name__
# call basal BasicGFF.togff() function
gfflines = [ BasicGFF.togff(self) ]
# gff default for TSS/ATG
tss_gff = { 'fref' : self._gff['fref'],
'gname' : self._gff['gname'],
'gclass': self._gff['gclass'], }
# if SignalPeptide is spliced -> make 2 tracks!
if self.intron:
# calculate lengths
signalp_length = self.end-self.start
signalp_5p_length = self.intron.donor.pos - self.start
signalp_3p_length = signalp_length - signalp_5p_length
# create SignalP 5p and 3p tracks
exon5p = list(gfflines[0])
exon3p = list(gfflines[0])
exon5p[4] = self.intron.donor.pos
exon3p[3] = self.intron.acceptor.pos + 1
exon3p[4] = self.intron.acceptor.pos + signalp_3p_length
if self.tss: exon5p[3]+=3
gfflines = [ tuple(exon5p), tuple(exon3p) ]
if self.tss: gfflines.insert(0, self.tss.togff(gff=tss_gff) )
elif self.tss:
# correct SignalPeptide start coord to 1nt after the ATG codon
track = list(gfflines[0])
track[3]+=3
gfflines = [ tuple(track) ]
gfflines.insert(0, self.tss.togff(gff=tss_gff) )
else:
pass
# return list with gff tuples
return gfflines
def togff(self,gff={}):
""" Overwrites BasicGFF.togff() """
if not gff.has_key('gname'): gff['gname'] = str(self.pos)
return BasicGFF.togff(self,gff=gff)
def togff(self,gff={}):
""" Overwrites BasicGFF.togff() """
if not gff.has_key('gname') and not self._gff.has_key('gname'):
gff['gname'] = "%s-%s" % (self.start, self.end)
return BasicGFF.togff(self,gff=gff)
def togff(self, gff={}):
""" Overwrites BasicGFF.togff() """
if not gff.has_key('gname'): gff['gname'] = str(self.pos)
return BasicGFF.togff(self, gff=gff)
