I just ran this over the weekend
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Bacteria;Cyanobacteria_Chloroplast;Chloroplast-Mitochondria-unknown-Eukaryota) in my batch file but my final taxonomy file still included chloroplasts. Am I missing something obvious? This is a script we’ve been using a long time so I’m confused as to why I’m suddenly seeing chloroplasts again.
EDIT: So it appears that it IS obvious. We were seeing chloroplasts SPECIFICALLY in the cyanobacteria_chloroplast hybrid phylum before, so that’s why our code was written the way it was. I mistakenly thought I was also following Pat’s advice and selecting for chloroplasts in general, but in my code, you can see that the only chloroplasts I was removing were in that “Class.” Once I added an additional bit to include chloroplasts in general, it was fixed.
remove.lineage(fasta=current, count=current, taxonomy=current, taxon=Bacteria;Cyanobacteria_Chloroplast;Chloroplast-Chloroplast-Mitochondria-unknown-Eukaryota