API Reference

Squiggle is built around a single function, documented fully below:

squiggle.transform(sequence, method='squiggle', bar=False)

Transforms a DNA sequence into a series of coordinates for 2D visualization.

Parameters:
  • sequence (str) – The DNA sequence to transform.
  • method (str) – The method by which to transform the sequence. Defaults to “squiggle”. Valid options are squiggle, gates, yau, randic and qi.
  • bar (bool) – Whether to display a progress bar. Defaults to false.
Returns:

A tuple containing two lists: one for the x coordinates and one for the y coordinates.
Return type:

tuple

Example

>>> transform("ATGC")
([0.0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0], [0, 0.5, 0, -0.5, -1, -0.5, 0, -0.5, 0])
>>> transform("ATGC", method="gates")
([0, 0, 0, 1, 0], [0, -1, 0, 0, 0])
>>> transform("ATGC", method="yau")
([0, 0.5, 1.0, 1.8660254037844386, 2.732050807568877], [0, -0.8660254037844386, 0.0, -0.5, 0.0])
>>> transform("ATGC", method="yau-bp")
([0, 1, 2, 3, 4], [0, -1, 0, -0.5, 0.0])
>>> transform("ATGC", method="randic")
([0, 1, 2, 3], [3, 2, 1, 0])
>>> transform("ATGC", method="qi")
([0, 1, 2], [8, 7, 11])

Warning

The entire sequence must be able to fit in memory.

Raises:ValueError – When an invalid character is in the sequence.