A simple library to store and query genomic features and sequence. Find neighbors of a given feature up or downstream, or on a given strand. Use a feature to slice out sequence from an associated fasta file.

Genedex uses numpy memmaped arrays for fasta slicing of fasta files without creating an new (often very large) sequence file. Instead, it creates a .gdx which is a pickled dictionary where the keys are the headers and the values are the start, stop positions of the sequence in the fasta file.

To do fast feature queries, genedex uses rtree. This does nearest neighbor and overlap queries very efficiently. This requires a n install of spatialindex as described here

Read the HTML documentation here: http://genedex.googlecode.com/svn/trunk/doc/readme.html

After installing SpatialIndex Install with easy_install:

sudo easy_install http://genedex.googlecode.com/svn/trunk/