def _make_position(location_string, offset=0):
"""Turn a Swiss location position into a SeqFeature position object (PRIVATE).
An offset of -1 is used with a start location to make it pythonic.
"""
if location_string == "?":
return SeqFeature.UnknownPosition()
#Hack so that feature from 0 to 0 becomes 0 to 0, not -1 to 0.
try:
return SeqFeature.ExactPosition(max(0, offset + int(location_string)))
except ValueError:
pass
if location_string.startswith("<"):
try:
return SeqFeature.BeforePosition(
max(0, offset + int(location_string[1:])))
except ValueError:
pass
elif location_string.startswith(">"): # e.g. ">13"
try:
return SeqFeature.AfterPosition(
max(0, offset + int(location_string[1:])))
except ValueError:
pass
elif location_string.startswith("?"): # e.g. "?22"
try:
return SeqFeature.UncertainPosition(
max(0, offset + int(location_string[1:])))
except ValueError:
pass
raise NotImplementedError("Cannot parse location '%s'" % location_string)
def _parse_position(element, offset=0):
try:
position = int(element.attrib['position']) + offset
except KeyError as err:
position = None
status = element.attrib.get('status', '')
if status == 'unknown':
assert position is None
return SeqFeature.UnknownPosition()
elif not status:
return SeqFeature.ExactPosition(position)
elif status == 'greater than':
return SeqFeature.AfterPosition(position)
elif status == 'less than':
return SeqFeature.BeforePosition(position)
elif status == 'uncertain':
return SeqFeature.UncertainPosition(position)
else:
raise NotImplementedError("Position status %r" % status)