Added in some extra logic into parse_sam to recruit extra reads
If a read is mapped but falls below the percent identity threshold
it would be lost to segregation.  Those reads are now added to
the 'root' taxon for unmapped reads
Added in a bowtie-build class
Added in a convenience function to return a list of output files
This is a feature of the PyCogent app controllers that is lacking
in Biopython.  The function returns a dictionary of all the files
that were created by phrap for easy opening and use
fixed a PEP8 error
Added in code for generating an OTU table based on the fpkc value
The current scheme is to collect of the full length sequences and
then call out to qiime to pick the otus and rep set.  The taxonomy
is then assigned using bowtie and a biom-format OTU table is generated