Silva 99 (v132) parsing issue.

[grabearummc]

When running Silva 99 (v132) with the Nephele 16S Qiime pipeline, taxonomy may or may not contain spaces (instead of NAs??). Regardless, the spaces are parsed and a Rank column is added. This leads to redundant columns in the dataset (Rank1-Rank7), which is introduced after the first line (

MicrobiomeR/R/phyloseq.R

Line 286 in dfc8f67

char.vec <- phyloseq::parse_taxonomy_default(char.vec)

)

Another parser needs to be created, or the function needs to be adopted and renamed.