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Represent a Sequence Feature holding info about a part of a sequence. This is heavily modeled after the Biocorba SeqFeature objects, and may be pretty biased towards GenBank stuff since I'm writing it for the GenBank parser output... What's here: Base class to hold a Feature. ---------------------------- classes: o SeqFeature Hold information about a Reference. ---------------------------------- This is an attempt to create a General class to hold Reference type information. classes: o Reference Specify locations of a feature on a Sequence. --------------------------------------------- This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in much the same way as Biocorba. This has the advantages of allowing us to handle fuzzy stuff in case anyone needs it, and also be compatible with Biocorba. classes: o FeatureLocation - Specify the start and end location of a feature. o ExactPosition - Specify the position as being exact. o WithinPosition - Specify a position occuring within some range. o BetweenPosition - Specify a position occuring between a range. o BeforePosition - Specify the position as being found before some base. o AfterPosition - Specify the position as being found after some base.
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SeqFeature Represent a Sequence Feature on an object. |
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Reference Represent a Generic Reference object. |
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FeatureLocation Specify the location of a feature along a sequence. |
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AbstractPosition Abstract base class representing a position. |
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ExactPosition Specify the specific position of a boundary. |
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WithinPosition Specify the position of a boundary within some coordinates. |
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BetweenPosition Specify the position of a boundary between two coordinates. |
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BeforePosition Specify a position where the actual location occurs before it. |
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AfterPosition Specify a position where the actual location is found after it. |
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OneOfPosition Specify a position where the location can be multiple positions. |
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PositionGap Simple class to hold information about a gap between positions. |
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__package__ = None hash(x) |
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