#pre.cluster
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# fasta=stability.trim.contigs.good.unique.good.filter.unique.fasta, count=stability.trim.contigs.good.unique.good.filter.count_table,from MISeq_SOP
set.dir(input=./TestFiles, output=./pre.cluster, tempdefault=./TestReferences)
set.logfile(name=precluster.logfile)
pre.cluster(fasta=testPrecluster.fasta, count=testPrecluster.count_table, diffs=2)
summary.seqs(count=current)
pre.cluster(fasta=testPrecluster.fasta, count=testPrecluster.count_table, diffs=2, method=unoise)
summary.seqs(count=current)
pre.cluster(fasta=testPrecluster.fasta, count=testPrecluster.count_table, diffs=2, method=tree)
summary.seqs(count=current)
pre.cluster(fasta=testPrecluster.fasta, count=testPrecluster.count_table, diffs=2, method=deblur)
summary.seqs(count=current)
#test unaligned clustering
pre.cluster(fasta=testPrecluster.ng.fasta, count=testPrecluster.count_table, diffs=2)
summary.seqs(count=current)
pre.cluster(fasta=testPrecluster.names_groups.fasta, name=testPrecluster.names, group=testPrecluster.groups, diffs=2)
summary.seqs(count=current)
quit()

