give final file format options

[rrohwer]

right now the final taxonomy file is generated in semicolon delimited format. This is closest to the mothur files, which are tab for the first column and then all semicolon. What do we want? Do people use that format for something? Or should we just make it a csv to save everyone a little bit of a headache?

[rrohwer]

AND, do we want to add in a total reads column. I recall the one I worked with on the TAGs before had that added in. I already generate a list of reads for each seqID, it's just not included.

[rrohwer]

note that mothur has a step after classify.seqs called remove.lineage that removes all the chloroplast, mitochondria, unknown, archaea, and eukaryota. Could reformat into mothur format, or that's pretty easy to just do ourselves too.

[rrohwer]

update: right now the final taxonomy file is .csv delimited, with headers, and without any "totals" columns. I still need to add something to remove the archaea and other crap.

[rrohwer]

maybe just have a flag: rds csv semicolon mothur(tab/semicolon)