script support

It would be really KILLER if there were some sort of primitive scripting support in mothur. For example, I’d love to be able to do this:

for i in {1..16}; do 
    get.seqs(accnos=W${i}.groups,fasta=auw.msa.unique.fa);
    classify.seqs(fasta=auw.msa.unique.pick.fa,template=silva.bacteria.fasta, taxonomy=silva.full.taxonomy,processors=2)
    system(mv auw.msa.unique.pick.silva.full.taxonomy W${i}.silva.full.taxonomy;
    system( mv auw.msa.unique.pick.silva.full.tax.summary W${i}.silva.full.tax.summary;
done;

I do it now by writing a script to generate a mothur batch control file. But that’s ugly.