#screen.seqs
# NOTE: download TestReferences and TestFiles and put in same location as mothur executable
# screenSeqs.fasta is stability.trim.contigs.fasta from MISeq_SOP
# screenSeqs.groups is stability.contigs.groups from MISeq_SOP
# screenSeqs.summary is stability.trim.contigs.summary from MISeq_SOP
# screenSeqs.contigs.report is stability.contigs.report from MISeq_SOP
# screenSeqs2.align is stability.trim.contigs.good.unique.align from MISeq_SOP
# screenSeqs2.count_table is stability.trim.contigs.good.count_table from MISeq_SOP
# screenSeqs2.summary is stability.trim.contigs.good.unique.summary from MISeq_SOP
set.dir(input=./TestFiles, output=./TestResults/screen.seqs, tempdefault=./TestReferences)
set.logfile(name=screen.seqs.logfile)
#screening after make.contigs
screen.seqs(fasta=screenSeqs.fasta, group=screenSeqs.groups, maxambig=0, maxlength=275)
screen.seqs(fasta=screenSeqs.fasta, group=screenSeqs.groups, summary=screenSeqs.summary, maxambig=0, maxlength=275)
#screening after alignment
screen.seqs(fasta=screenSeqs2.align, count=screenSeqs2.count_table, start=1968, end=11550, maxhomop=8)
screen.seqs(fasta=screenSeqs2.align, count=screenSeqs2.count_table, summary=screenSeqs2.summary, start=1968, end=11550, maxhomop=8)
#additional parameters testing
screen.seqs(fasta=screenSeqs2.align, count=screenSeqs2.count_table, optimize=start-end-maxambig, criteria=90)
screen.seqs(fasta=screenSeqs.fasta, group=screenSeqs.groups, contigsreport=screenSeqs.contigs.report, mismatches=5)
screen.seqs(fasta=screenSeqs.fasta, group=screenSeqs.groups, contigsreport=screenSeqs.contigs.report, minoverlap=25)
screen.seqs(fasta=screenSeqs.fasta, group=screenSeqs.groups, contigsreport=screenSeqs.contigs.report, optimize=ostart-oend, criteria=90)
screen.seqs(fasta=screenSeqs2.align, count=screenSeqs2.count_table, alignreport=screenSeqs2.align.report, minscore=60, maxinsert=5, minsim=90)
screen.seqs(fasta=screenSeqs2.align, count=screenSeqs2.count_table, summary=screenSeqs2.summary, start=1968, end=11550, maxhomop=8)

quit()
