#cluster.split
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# testCluster.fasta is stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.pick.fasta from MiSeq_SOP
# testCluster.count is , count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.pick.pick.count_table from MiSeq_SOP
# testCluster.taxonomy is , taxonomy=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.pick.taxonomy from MiSeq_SOP
# test different cluster methods and seaches
#set.dir(input=./TestFiles, output=./TestResults/cluster.split, tempdefault=./TestReferences)
set.dir(input=/Users/swestcott/Desktop/release)
set.logfile(name=clustersplit.logfile)
cluster.split(fasta=testCluster.fasta, count=testCluster.count_table, taxonomy=testCluster.taxonomy, taxlevel=4, cutoff=0.03)
cluster.split(fasta=testCluster.fasta, count=testCluster.count_table, taxonomy=testCluster.taxonomy, taxlevel=4, cutoff=0.03, method=agc)
cluster.split(fasta=testCluster.fasta, count=testCluster.count_table, taxonomy=testCluster.taxonomy, taxlevel=4, cutoff=0.03, method=dgc)
cluster.split(fasta=testCluster.fasta, count=testCluster.count_table, taxonomy=testCluster.taxonomy, taxlevel=4, cutoff=0.03, cluster=f)
cluster.split(file=current)
cluster.split(fasta=UNITEv6_sh_97.fasta, count=UNITEv6_sh_97.count_table, taxonomy=UNITEv6_sh_97.tax, cutoff=0.03)
quit()

