Bio.Util: Utility Functions

The Bio.Util module provides utility functions commonly used in bioinformatics.

Labelled square matrix parsers

This module contains a function readlsm, that reads labelled square matrices.

Such matrices are commonly used to store pairwise measures of similarity or dissimilarity between two sets. This format consists of a delimited file, with text labels on the upper and left sides of a square matrix. Such matrices are often but not exclusively symmetric.

An example would be:

    A   B
A   1   2
B   2   1

(Note that we use spaces as a delimiter, where tabs would normally be used)