Hello all. This may be a bit off topic for this thread but I think I've come up with a way to provide clean Greengenes-like taxonomy formatting for the SILVA reference sequences. For example, here is some on-screen output from some prototype code I've written to parse the d,k,p,c,o,f,g ranks:
d__Eukaryota; k__Stramenopiles; p__Ochrophyta; c__Xanthophyceae; o__Mischococcales; g__Bumilleriopsis AM491616.1.1802
d__Eukaryota; k__Stramenopiles; p__Ochrophyta; c__Xanthophyceae; o__Mischococcales; g__Chlorellidium FJ030892.1.1781
d__Eukaryota; k__Stramenopiles; p__Ochrophyta; c__Xanthophyceae; o__Mischococcales; g__Mischococcus AF083400.1.1806
d__Eukaryota; k__Stramenopiles; p__Ochrophyta; c__Xanthophyceae; o__Mischococcales; g__Pleurochloris AF109728.1.1788
I've been working on this a little each day and I still have some minor details to work out. But hopefully it is a start. Once I have the prototype code complete I'll upload and link it via the forum. The solution appears to be embarrassingly easy.
-Best
-Mike