produce table of lineages represented as taxonomic names

[nhoffman]

Two use cases for the output:

• the csv file can be used to construct a phyloseq object
• the ".taxonomy" format (https://mothur.org/wiki/Taxonomy_File) can be used as an input to the MOTHUR naive bayes classifier

The format for the latter seems to vary from place to place. Here's an example of what I arrived at:

s1  "pk__Bacteria";"ph__Firmicutes";"cl__Bacilli";"or__Bacillales";"fa__Staphylococcaceae";"ge__Staphylococcus";"sp__Staphylococcus aureus"
s2  "pk__Bacteria";"ph__Firmicutes";"cl__Bacilli";"or__Bacillales";"fa__Staphylococcaceae";"ge__Staphylococcus";"sp__Staphylococcus equorum"
s3  "pk__Bacteria";"ph__Firmicutes";"cl__Bacilli";"or__Bacillales";"fa__Staphylococcaceae";"ge__Staphylococcus";"sp__Staphylococcus equorum"
s4  "pk__Bacteria";"ph__Firmicutes";"cl__Bacilli";"or__Bacillales";"fa__Staphylococcaceae";"ge__Staphylococcus";"sp__unclassified"

[nhoffman]

done in version 0.8.5