get.coremicrobiome with lots of sets

Commands in mothur
1

I have a dataset with a bunch smaller sets of samples and I want to get the core microbiome for each of these smaller sets. would I need to run get.coremicrobiome for each set individually or is there a way to specify numerous sets?

i.e.

sample group
1 A
2 A
3 B
4 C
5 B
6 C

is there a way to say group=1-2,3-5, 4-6?

2

Unfortunately, mothur does not have a way to indicate sets of groups to process at this point. You could try something like this in a batch file:

get.coremicrobiome(shared=yourSharedFile, groups=1-2)
get.coremicrobiome(shared=yourSharedFile, groups=3-4-5)
get.coremicrobiome(shared=yourSharedFile, groups=4-5-6)

3

do I need to rename between each get.coremicrobiome?