biopython v1.71.0 Bio.SeqFeature.BetweenPosition

Specify the position of a boundary between two coordinates (OBSOLETE?).

Arguments:

  • position - The default integer position
  • left - The start (left) position of the boundary
  • right - The end (right) position of the boundary

This allows dealing with a position like 123^456. This indicates that the start of the sequence is somewhere between 123 and 456. It is up to the parser to set the position argument to either boundary point (depending on if this is being used as a start or end of the feature). For example as a feature end:

 >>> p = BetweenPosition(456, 123, 456)
 >>> p
 BetweenPosition(456, left=123, right=456)
 >>> print(p)
 (123^456)
 >>> int(p)
 456

Integer equality and comparison use the given position,

 >>> p == 456
 True
 >>> p in [455, 456, 457]
 True
 >>> p > 300
 True

The old legacy properties of position and extension give the starting/lower/left position as an integer, and the distance to the ending/higher/right position as an integer. Note that the position object will act like either the left or the right end-point depending on how it was created:

 >>> p2 = BetweenPosition(123, left=123, right=456)
 >>> p.position == p2.position == 123
 True
 >>> p.extension
 333
 >>> p2.extension
 333
 >>> p.extension == p2.extension == 333
 True
 >>> int(p) == int(p2)
 False
 >>> p == 456
 True
 >>> p2 == 123
 True

Note this potentially surprising behaviour:

 >>> BetweenPosition(123, left=123, right=456) == ExactPosition(123)
 True
 >>> BetweenPosition(123, left=123, right=456) == BeforePosition(123)
 True
 >>> BetweenPosition(123, left=123, right=456) == AfterPosition(123)
 True

i.e. For equality (and sorting) the position objects behave like integers.

Link to this section Summary

Functions

Create a new instance in BetweenPosition object

Represent the BetweenPosition object as a string for debugging

Return a representation of the BetweenPosition object (with python counting)

Return a copy of the location after the parent is reversed (PRIVATE)

Return a copy of the position object with its location shifted (PRIVATE)

Legacy attribute to get extension (from left to right) as an integer (OBSOLETE)

Legacy attribute to get (left) position as integer (OBSOLETE)

Link to this section Functions

Create a new instance in BetweenPosition object.

Represent the BetweenPosition object as a string for debugging.

Return a representation of the BetweenPosition object (with python counting).

Return a copy of the location after the parent is reversed (PRIVATE).

Return a copy of the position object with its location shifted (PRIVATE).

Legacy attribute to get extension (from left to right) as an integer (OBSOLETE).

Legacy attribute to get (left) position as integer (OBSOLETE).