import_qiime(): Add GreenGenes and other alternative ref seq database options about phyloseq

[joey711]

GreenGenes does not appear to label strains. This column can be left NA in the taxonomy table.

[joey711]

SILVA is another popular reference database. Should add an import option for that style of taxonomic annotation.

It appears tab-delimited like this:

OTU_ID SILVA_short_name DOMAIN PHYLUM CLASS ORDER FAMILY GENUS SPECIES
31717 uncultured bacterium Bacteria Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae
32041 uncultured bacterium Bacteria Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae
32252 uncultured bacterium Bacteria Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae
35213 uncultured bacterium Bacteria Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae
35797 uncultured bacterium Bacteria Acidobacteria Acidobacteria Acidobacteriales Acidobacteriaceae

[joey711]

This was partially tackled while adding support for BIOM format, which is where QIIME is headed, anyway. May not be worth the effort to add this feature for "old" import_qiime(), since it is already available (I think) for import_biom().

Need to check the extent that "green-genes" is supported, and perhaps add the SILVA option. I think the green-genes approach is already modular, so it shouldn't be hard to add the SILVA option in the same way.

[joey711]

This is supported through a parse_qiime_tax_string and parseGreenGenesPrefix internal functions. Might consider opening these up as user-exposed functions at some stage if you ever give them tests, doc, and further devel for other reference formats besides greengenes; and also when you finally split phyloseq into separate IO and analysis packages

Otherwise, this issue is closed (and should have been a while ago, I think).