def __init__(self,seqerrorstart,seqerrorend,gff={}):
# input validation
if type(seqerrorstart) == type(int()):
seqerrorstart = SequenceErrorCoordinate(seqerrorstart)
else:
IsSequenceErrorCoordinate(seqerrorstart)
if type(seqerrorend) == type(int()):
seqerrorend = SequenceErrorCoordinate(seqerrorend)
else:
IsSequenceErrorCoordinate(seqerrorend)
# initialization
BasicGFF.__init__(self)
self._gff.update(gff)
self.donor = seqerrorstart
self.acceptor = seqerrorend
self.length = self.acceptor.pos-self.donor.pos
self.start = self.donor.pos
self.end = self.acceptor.pos
self.typeof = None
# Estimated coordinate of this sequence error
# It is possible to pinpoint this SequenceError to a certain
# position but (re)label the estimated coordinate somewhere is.
# This option is needed in ABFGP in case of Intertions/Deletions
self._estimated_nt_coord = self.donor.pos
# set shared nt/aa data. This mimmics attributes from
# the Intron class and maintains readingframe in a genestructure
self.shared_nts = "nnn"
self.shared_aa = "X"
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)
self._gff['column9data']['typeof'] = self.typeof
retgff = {}
retgff.update(self._gff)
retgff.update(gff)
return BasicGFF.togff(self,gff=retgff)