Package Bio :: Module SeqFeature
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Module SeqFeature

source code

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.
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classes:
o SeqFeature

Hold information about a Reference.
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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.
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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 CompoundLocation - Collection of FeatureLocation objects (for joins etc).

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 (OBSOLETE?).
o BeforePosition - Specify the position as being found before some base.
o AfterPosition - Specify the position as being found after some base.
o OneOfPosition - Specify a position where the location can be multiple positions.
o UnknownPosition - Represents missing information like '?' in UniProt.

Classes [hide private]
  SeqFeature
Represent a Sequence Feature on an object.
  Reference
Represent a Generic Reference object.
  FeatureLocation
Specify the location of a feature along a sequence.
  CompoundLocation
For handling joins etc where a feature location has several parts.
  AbstractPosition
Abstract base class representing a position.
  ExactPosition
Specify the specific position of a boundary.
  UncertainPosition
Specify a specific position which is uncertain.
  UnknownPosition
Specify a specific position which is unknown (has no position).
  WithinPosition
Specify the position of a boundary within some coordinates.
  BetweenPosition
Specify the position of a boundary between two coordinates (OBSOLETE?).
  BeforePosition
Specify a position where the actual location occurs before it.
  AfterPosition
Specify a position where the actual location is found after it.
  OneOfPosition
Specify a position where the location can be multiple positions.
  PositionGap
Simple class to hold information about a gap between positions.
Variables [hide private]
  __package__ = 'Bio'