biopython v1.71.0 Bio.SeqFeature.WithinPosition

Specify the position of a boundary within some coordinates.

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 ((1.4)..100). This indicates that the start of the sequence is somewhere between 1 and 4. Since this is a start coordinate, it should acts like it is at position 1 (or in Python counting, 0).

 >>> p = WithinPosition(10, 10, 13)
 >>> p
 WithinPosition(10, left=10, right=13)
 >>> print(p)
 (10.13)
 >>> int(p)
 10

Basic integer comparisons and operations should work as though this were a plain integer:

 >>> p == 10
 True
 >>> p in [9, 10, 11]
 True
 >>> p < 11
 True
 >>> p + 10
 20

 >>> isinstance(p, WithinPosition)
 True
 >>> isinstance(p, AbstractPosition)
 True
 >>> isinstance(p, int)
 True

Note this also applies for comparison to other position objects, where again the integer behaviour is used:

 >>> p == 10
 True
 >>> p == ExactPosition(10)
 True
 >>> p == BeforePosition(10)
 True
 >>> p == AfterPosition(10)
 True

If this were an end point, you would want the position to be 13:

 >>> p2 = WithinPosition(13, 10, 13)
 >>> p2
 WithinPosition(13, left=10, right=13)
 >>> print(p2)
 (10.13)
 >>> int(p2)
 13
 >>> p2 == 13
 True
 >>> p2 == ExactPosition(13)
 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:

 >>> p.position == p2.position == 10
 True
 >>> p.extension == p2.extension == 3
 True
 >>> int(p) == int(p2)
 False
 >>> p == 10
 True
 >>> p2 == 13
 True

Link to this section Summary

Functions

Create a WithinPosition object

Represent the WithinPosition object as a string for debugging

Return a representation of the WithinPosition 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 WithinPosition object.

Represent the WithinPosition object as a string for debugging.

Return a representation of the WithinPosition 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).