#classify.seqs
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# testClassify.fasta is stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.fasta from MiSeq_SOP
# testClassify.count is , count=stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.count_table from MiSeq_SOP
# test different classification methods and seaches
set.dir(input=./TestFiles, output=./classify.seqs, tempdefault=./TestReferences)
set.logfile(name=classifyseqs.logfile)
classify.seqs(fasta=testClassify.fasta, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax)
classify.seqs(fasta=testClassify.fasta, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, relabund=t)
classify.seqs(fasta=testClassify.fasta, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, probs=f)
classify.seqs(fasta=testClassify.fasta, count=testClassify.count_table, reference=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax)
#
#knn
classify.seqs(fasta=testClassify.fasta, template=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, method=knn)
classify.seqs(fasta=testClassify.fasta, count=testClassify.count_table, template=trainset9_032012.pds.fasta, taxonomy=trainset9_032012.pds.tax, method=knn, search=blast)
quit()
