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:

• SeqFeature

Hold information about a Reference

This is an attempt to create a General class to hold Reference type information.

Classes:

• Reference

Specify locations of a feature on a Sequence

This aims to handle, in Ewan Birney’s words, ‘the dreaded fuzziness issue’. This has the advantages of allowing us to handle fuzzy stuff in case anyone needs it, and also be compatible with BioPerl etc and BioSQL.

Classes:

• FeatureLocation - Specify the start and end location of a feature.
• CompoundLocation - Collection of FeatureLocation objects (for joins etc).
• ExactPosition - Specify the position as being exact.
• WithinPosition - Specify a position occurring within some range.
• BetweenPosition - Specify a position occurring between a range (OBSOLETE?).
• BeforePosition - Specify the position as being found before some base.
• AfterPosition - Specify the position as being found after some base.
• OneOfPosition - Specify a position where the location can be multiple positions.
• UnknownPosition - Represents missing information like ‘?’ in UniProt.