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Consistent output for SortMeRNA tax assignment
The script assign_taxonomy.py -m sortmerna
works great! However, the resulting taxonomy sometimes omits unassigned levels.
In this output, g__; s__
should be at the end of the second line, but is not. It is at the end of the last line, which is strangely inconsistent. (Scroll to the right :point_right: )
OTU_1size=568804 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Oxalobacteraceae; g__Ralstonia; s__ 0.80 5
OTU_2size=174442 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae 1.00 5
OTU_3size=125310 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Bradyrhizobiaceae 1.00 4
OTU_4size=106515 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Nitrosomonadales; f__Nitrosomonadaceae 0.75 4
OTU_5size=102290 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 1.00 5
I have not taken a look at the code yet, but I'm interested in taking this one.