Class FeatureLocation
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object --+
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FeatureLocation
Specify the location of a feature along a sequence.
This attempts to deal with fuzziness of position ends, but also make
it easy to get the start and end in the 'normal' case (no fuzziness).
You should access the start and end attributes with
your_location.start and your_location.end. If the start and end are
exact, this will return the positions, if not, we'll return the
approriate Fuzzy class with info about the position and fuzziness.
Note that the start and end location numbering follow Python's scheme,
thus a GenBank entry of 123..150 (one based counting) becomes a location
of [122:150] (zero based counting).
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__str__(self)
Returns a representation of the location (with python counting). |
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_shift(self,
offset)
Returns a copy of the location shifted by the offset (PRIVATE). |
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Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__setattr__ ,
__sizeof__ ,
__subclasshook__
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start
Start location (possibly a fuzzy position, read only).
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end
End location (possibly a fuzzy position, read only).
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nofuzzy_start
Start position (integer, approximated if fuzzy, read only).
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nofuzzy_end
End position (integer, approximated if fuzzy, read only).
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Inherited from object :
__class__
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Specify the start and end of a sequence feature.
start and end arguments specify the values where the feature begins
and ends. These can either by any of the *Position objects that inherit
from AbstractPosition, or can just be integers specifying the position.
In the case of integers, the values are assumed to be exact and are
converted in ExactPosition arguments. This is meant to make it easy to
deal with non-fuzzy ends.
- Overrides:
object.__init__
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__str__(self)
(Informal representation operator)
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Returns a representation of the location (with python counting).
For the simple case this uses the python splicing syntax, [122:150]
(zero based counting) which GenBank would call 123..150 (one based
counting).
- Overrides:
object.__str__
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A string representation of the location for debugging.
- Overrides:
object.__repr__
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start
Start location (possibly a fuzzy position, read only).
- Get Method:
- unreachable(self)
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end
End location (possibly a fuzzy position, read only).
- Get Method:
- unreachable(self)
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nofuzzy_start
Start position (integer, approximated if fuzzy, read only).
To get non-fuzzy attributes (ie. the position only) ask for
'location.nofuzzy_start', 'location.nofuzzy_end'. These should return the
largest range of the fuzzy position. So something like: (10.20)..(30.40)
should return 10 for start, and 40 for end.
- Get Method:
- _get_nofuzzy_start(self)
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nofuzzy_end
End position (integer, approximated if fuzzy, read only).
To get non-fuzzy attributes (ie. the position only) ask for
'location.nofuzzy_start', 'location.nofuzzy_end'. These should return the
largest range of the fuzzy position. So something like: (10.20)..(30.40)
should return 10 for start, and 40 for end.
- Get Method:
- _get_nofuzzy_end(self)
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