This code is meant to ease the processes involved in performing a k-mer analysis
for use as a classification device to determine phylum of origin of a metagenomic
sample. There are currently 4 pieces of code in this project.

degenate.py - This code reads in a short nucleotide sequence and determines if 
 there's degeneracy (i.e. B is "Not A") and returns the possible sequences of the 
 given length that could have resulted in the degeneracy. Use for sequencing data

Eukmer.py / kmer.py - The difference between these seems to be the input folder
 which is read. Both of these read through a sequence file, and come up with a 
 feature vector based on k-mer frequencies, using degenerate.py when appropriate
 to determine fractional frequencies when the kmer contains degenerate nucleotide(s)

seqselect.py - This code breaks up the "Euk" genome into 1000bp non-overlapping
 segments as described in the paper this is based on, so this can be read by
 Eukmer.py presumably to make the feature vectors.

The resulting feature vector files can then be handled in a different software,
in my case, I used matlab to produce Self Organizing Maps (or SOMs). With the 
feature information, sequences with similar kmer frequencies will cluster together, 
and are presumably from the same phylum.