Developer Interface

Main Interface

The main functionality consists of creating HMM sequence logos and saving them.

hmmlogo.get_svg(accession, **kwargs)

Returns a HMM sequence logo in SVG format.

Parameters

• accession (str) – Pfam accession for desired HMM.

• **kwargs – Additional arguments are passed to LogoPlot.

hmmlogo.save_svg(accession, fname, **kwargs)

Writes an HMM sequence logo to a file in SVG format.

Parameters

• accession (str) – Pfam accession for desired HMM.

• fname (str or file-like object) – A path or a Python file-like object.

Classes

class hmmlogo.LogoPlot(accession, alph=None, cmap=None)

Class that creates figure of a profile hidden Markov model.

Parameters

• accession (str) – Pfam accession for desired HMM.

• alph (str, optional) – Path to alphabet (defaults to alphabet located in library).

• cmap (str, optional) – Path to colormap (defaults to color map located in library).