the format of groups file

Hi guys,

I am using mothur for a while. Now one issue really toubles me. I made a mistake in making the groups file in the begining with - , for example, co-1,co-2. It went well for the whole process. However, now I need to get some special groups from the fasta file, it failed due to the wrong format with get.groups. I don`t want to process the data from the first step again.

Any help is greatly appreciated!

Best wishes


You can escape the dashes in the group names or file names. For example:

get.groups(group=testdash.groups, groups=c1-0-c1-2)

would select the groups c1-0 and c1-2.

Thanks Westcott for your help.
It works well.