General tools:

• ConfigParsers : tools for handy parsing of the .ini functions. Instead of costum data structure returns a dict

• Dataviz: a set of somewhat more involved functions for data showing * violin plot * better 2-D density plot

• Dictionary comparator: fuzzy dictionary comparator

• Linalg routines: useful, but somewhat uncommon linear algebra operations

• GDF exprot: converts a matrix representation of a graph to a GDF format, plus assigns properties to all the nodes.

• Xml Doctor: a tool that is usefull to inspect what is truly contained in an xml file: number of class instances, fields for each instance and classes of fields. The one here has been optimzied for Reactome BioPax Lvl3 analysis

• Matrix 2D embedding: transform a distance matrix to a 2-D representation.

• buffered methods : a set of methods for rapid dumping/undumping of objects that need to be injected into a class to make it buffered. usefull for rapid iterations on classes with long intermediary computation times.

Tools specific to bioinformatics:

• Uniprot/Go structure parsers : useful parsers for biology that parse aliases and relations to a dict format.

author : chiffa@github.com Some of the tools are courtesy of StackOverflow answers that are usually cited in the comments.

Most of metods rely heavily on numpy, scipy, and scikits-learn