Package Bio :: Module SeqFeature :: Class FeatureLocation
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Class FeatureLocation

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object --+
         |
        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).

Instance Methods [hide private]
 
__init__(self, start, end)
Specify the start and end of a sequence feature.
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__str__(self)
Returns a representation of the location (with python counting).
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__repr__(self)
A string representation of the location for debugging.
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_shift(self, offset)
Returns a copy of the location shifted by the offset (PRIVATE).
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_get_nofuzzy_start(self) source code
 
_get_nofuzzy_end(self) source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Properties [hide private]
  start
Start location (possibly a fuzzy position, read only).
  end
End location (possibly a fuzzy position, read only).
  nofuzzy_start
Start position (integer, approximated if fuzzy, read only).
  nofuzzy_end
End position (integer, approximated if fuzzy, read only).

Inherited from object: __class__

Method Details [hide private]

__init__(self, start, end)
(Constructor)

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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__

__str__(self)
(Informal representation operator)

source code 

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__

__repr__(self)
(Representation operator)

source code 

A string representation of the location for debugging.

Overrides: object.__repr__

Property Details [hide private]

start

Start location (possibly a fuzzy position, read only).

Get Method:
unreachable(self)

end

End location (possibly a fuzzy position, read only).

Get Method:
unreachable(self)

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)

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)