def _parse_alt(self, str):
if re.search('[\[\]]', str) is not None:
# Paired breakend
items = re.split('[\[\]]', str)
remoteCoords = items[1].split(':')
chr = remoteCoords[0]
if chr[0] == '<':
chr = chr[1:-1]
withinMainAssembly = False
else:
withinMainAssembly = True
pos = remoteCoords[1]
orientation = (str[0] == '[' or str[0] == ']')
remoteOrientation = (re.search('\[', str) is not None)
if orientation:
connectingSequence = items[2]
else:
connectingSequence = items[0]
return _Breakend(chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly)
elif str[0] == '.' and len(str) > 1:
return _SingleBreakend(True, str[1:])
elif str[-1] == '.' and len(str) > 1:
return _SingleBreakend(False, str[:-1])
elif str[0] == "<" and str[-1] == ">":
return _SV(str[1:-1])
else:
return _Substitution(str)
def _parse_alt(self, str):
if re.search('[\[\]]', str) is not None:
# Paired breakend
items = re.split('[\[\]]', str)
remoteCoords = items[1].split(':')
chr = remoteCoords[0]
if chr[0] == '<':
chr = chr[1:-1]
withinMainAssembly = False
else:
withinMainAssembly = True
pos = remoteCoords[1]
orientation = (str[0] == '[' or str[0] == ']')
remoteOrientation = (re.search('\[', str) is not None)
if orientation:
connectingSequence = items[2]
else:
connectingSequence = items[0]
return _Breakend(chr, pos, orientation, remoteOrientation, connectingSequence, withinMainAssembly)
elif str[0] == '.' and len(str) > 1:
return _SingleBreakend(True, str[1:])
elif str[-1] == '.' and len(str) > 1:
return _SingleBreakend(False, str[:-1])
elif str[0] == "<" and str[-1] == ">":
return _SV(str[1:-1])
else:
return _Substitution(str)
