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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).
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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 |
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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. i.e. Short form: >>> from Bio.SeqFeature import FeatureLocation >>> loc = FeatureLocation(5,10) Explicit form: >>> from Bio.SeqFeature import FeatureLocation, ExactPosition >>> loc = FeatureLocation(ExactPosition(5),ExactPosition(10)) Other fuzzy positions are used similarly, >>> from Bio.SeqFeature import FeatureLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc2 = FeatureLocation(BeforePosition(5),AfterPosition(10))
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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).
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A string representation of the location for debugging.
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Returns True regardless of the length of the feature. This behaviour is for backwards compatibility, since until the __len__ method was added, a FeatureLocation always evaluated as True. Note that in comparison, Seq objects, strings, lists, etc, will all evaluate to False if they have length zero. WARNING: The FeatureLocation may in future evaluate to False when its length is zero (in order to better match normal python behaviour)! |
Returns the length of the region described by the FeatureLocation. Note that extra care may be needed for fuzzy locations, e.g. >>> from Bio.SeqFeature import FeatureLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10)) >>> len(loc) 5 |
Check if an integer position is within the FeatureLocation. Note that extra care may be needed for fuzzy locations, e.g. >>> from Bio.SeqFeature import FeatureLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10)) >>> len(loc) 5 >>> [i for i in range(15) if i in loc] [5, 6, 7, 8, 9] |
Iterate over the parent positions within the FeatureLocation. >>> from Bio.SeqFeature import FeatureLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc = FeatureLocation(BeforePosition(5),AfterPosition(10)) >>> len(loc) 5 >>> for i in loc: print i 5 6 7 8 9 >>> list(loc) [5, 6, 7, 8, 9] >>> [i for i in range(15) if i in loc] [5, 6, 7, 8, 9] |
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startStart location (possibly a fuzzy position, read only).
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endEnd location (possibly a fuzzy position, read only).
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nofuzzy_startStart 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.
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nofuzzy_endEnd 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.
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