for loops feeding a batch file?

I want to calculate alpha diversity for a list of taxa. I can make a file that has the desired taxa, feed that into a for loop something like this:

for t in taxa.file; do mothur #get.lineage(shared=final.shared, constaxonomy=final.cons.taxonomy, taxon=$t); summary.single(shared=current, size=1000, n=100); done

But, that would overwrite the new shared and alpha div files each time. Right? Is there another way to do this?

You could use mothur’s system command,, to rename the files so you don’t overwrite things.

ah, right. thanks