def _coreMapping(self):
"""
Build the Mapping ClassSerializer.
@return: Mapping ; A ClassSerializer object
@rtype: object
"""
Cross = self.makeCrossmap()
if not Cross:
return None
if self.parseTree.SingleAlleleVarSet:
mutations = [v.RawVar for v in self.parseTree.SingleAlleleVarSet]
elif self.parseTree.RawVar:
mutations = [self.parseTree.RawVar]
else:
self.__output.addMessage(
__file__, 4, 'ENOVARIANT',
'Variant description contains no mutation.')
return None
mappings = []
for mutation in mutations:
if not mutation.StartLoc:
self.__output.addMessage(__file__, 4, 'EUNKNOWN',
'Variant type not supported.')
return None
# Get the coordinates of the start position
startmain, startoffset, start_g = \
self._getcoords(Cross, mutation.StartLoc,
self.parseTree.RefType)
# If there is an end position, calculate the coordinates.
if mutation.EndLoc:
endmain, endoffset, end_g = \
self._getcoords(Cross, mutation.EndLoc,
self.parseTree.RefType)
else:
end_g, endmain, endoffset = start_g, startmain, startoffset
# Assign these values to the Mapping ClassSerializer
V = Mapping()
V.startmain = startmain
V.startoffset = startoffset
V.endmain = endmain
V.endoffset = endoffset
V.start_g = start_g
V.end_g = end_g
V.mutationType = mutation.MutationType
mappings.append(V)
return mappings
def _coreMapping(self):
"""
Build the Mapping ClassSerializer.
@return: Mapping ; A ClassSerializer object
@rtype: object
"""
Cross = self.makeCrossmap()
if not Cross:
return None
if self.parseTree.SingleAlleleVarSet:
mutations = [v.RawVar for v in self.parseTree.SingleAlleleVarSet]
else:
mutations = [self.parseTree.RawVar]
mappings = []
for mutation in mutations:
if not mutation.StartLoc:
return None
# Get the coordinates of the start position
startmain, startoffset, start_g = \
self._getcoords(Cross, mutation.StartLoc,
self.parseTree.RefType)
# If there is an end position, calculate the coordinates.
if mutation.EndLoc:
endmain, endoffset, end_g = \
self._getcoords(Cross, mutation.EndLoc,
self.parseTree.RefType)
else:
end_g, endmain, endoffset = start_g, startmain, startoffset
# Assign these values to the Mapping ClassSerializer
V = Mapping()
V.startmain = startmain
V.startoffset = startoffset
V.endmain = endmain
V.endoffset = endoffset
V.start_g = start_g
V.end_g = end_g
V.mutationType = mutation.MutationType
mappings.append(V)
return mappings
def mainMapping(self, accNo, mutation):
"""
One of the entry points (called by the HTML publisher).
@arg accNo: transcript (NM_) accession number (with version?)
@type accNo: unicode
@arg mutation: the 'mutation' (e.g. c.123C>T)
@type mutation: unicode
@return: ClassSerializer object
@rtype: object
"""
variant = "%s:%s" % (accNo, mutation)
if self._parseInput(variant):
acc = self.parseTree.LrgAcc or self.parseTree.RefSeqAcc
try:
version = int(self.parseTree.Version)
except ValueError:
version = None
self._get_mapping(acc, version)
mappings = self._coreMapping()
errors = []
for message in self.__output.getMessages():
soap_message = SoapMessage()
soap_message.errorcode = message.code
soap_message.message = message.description
errors.append(soap_message)
mapping = Mapping()
mapping.messages = errors
if not mappings: # Something went wrong
mapping.errorcode = len(errors)
return mapping
mapping.errorcode = 0
if len(mappings) == 1:
return mappings[0]
mapping.mutationType = 'compound'
# Now we have to do some tricks to combine the information from
# possibly multiple variants into one Mapping object.
# Todo: Maybe it is better to use self.mapping.orientation here.
min_g = 9000000000
max_g = 0
forward = True
for m in mappings:
if m.start_g > m.end_g:
forward = False
if m.start_g < min_g:
min_g = m.start_g
min_main = m.startmain
min_offset = m.startoffset
if m.end_g < min_g:
min_g = m.end_g
min_main = m.endmain
min_offset = m.endoffset
if m.start_g > max_g:
max_g = m.start_g
max_main = m.startmain
max_offset = m.startoffset
if m.end_g > max_g:
max_g = m.end_g
max_main = m.endmain
max_offset = m.endoffset
if forward:
mapping.startmain = min_main
mapping.startoffset = min_offset
mapping.endmain = max_main
mapping.endoffset = max_offset
mapping.start_g = min_g
mapping.end_g = max_g
else:
mapping.startmain = max_main
mapping.startoffset = max_offset
mapping.endmain = min_main
mapping.endoffset = min_offset
mapping.start_g = max_g
mapping.end_g = min_g
return mapping