+require 'maasha/biopieces'
+require 'maasha/fasta'
+
+SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
+
+class Uclust
+ include Enumerable
+
+ def initialize(infile, outfile, options)
+ @infile = infile
+ @outfile = outfile
+ @options = options
+ @command = []
+ end
+
+ # Method that calls Usearch sorting for sorting a FASTA file
+ # according to decending sequence length.
+ def sort
+ # usearch -sort seqs.fasta -output seqs.sorted.fasta
+ if File.size(@infile) < SORT_LIMIT
+ @command << "usearch --sort #{@infile} --output #{@infile}.sort"
+ else
+ @command << "usearch --mergesort #{@infile} --output #{@infile}.sort"
+ end
+
+ execute
+
+ File.rename "#{@infile}.sort", @infile
+ end
+
+ # Method to execute clustering de novo.
+ def cluster
+ @command << "usearch --cluster #{@infile} --uc #{@outfile} --id #{@options[:identity]}"
+
+ execute
+ end
+
+ # Method to execute database search.
+ def usearch
+ # usearch --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
+ @command << "usearch --query #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
+ @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
+
+ execute
+ end
+
+ # Method to execute clustering to database plus de novo if not matched.
+ def usearch_uclust
+ # usearch --cluster seqs_sorted.fasta --db db.fasta --uc results.uc --id 0.90
+ @command << "usearch --cluster #{@infile} --db #{@options[:database]} --uc #{@outfile} --id #{@options[:identity]}"
+
+ execute
+ end
+
+ # Method to parse a Uclust .uc file and for each line of data
+ # yield a Biopiece record.
+ def each
+ record = {}
+
+ File.open(@outfile, mode="r") do |ios|
+ ios.each_line do |line|
+ if line !~ /^#/
+ fields = line.chomp.split("\t")
+
+ record[:REC_TYPE] = "UCLUST"
+ record[:TYPE] = fields[0]
+ record[:CLUSTER] = fields[1].to_i
+ record[:SEQ_LEN] = fields[2].to_i
+ record[:IDENT] = fields[3].to_f
+ record[:STRAND] = fields[4]
+ record[:Q_BEG] = fields[5].to_i
+ record[:S_BEG] = fields[6].to_i
+ record[:S_END] = fields[6].to_i + fields[2].to_i
+ record[:CIGAR] = fields[7]
+ record[:Q_ID] = fields[8]
+ record[:S_ID] = fields[9]
+
+ yield record
+ end
+ end
+ end
+
+ self # conventionally
+ end
+
+ private
+
+ # Method to execute a command using a system() call.
+ # The command is composed of bits from the @command variable.
+ def execute
+ @command.unshift "nice -n 19"
+ @command << "--rev" if @options[:comp]
+ @command << "> /dev/null 2>&1" unless @options[:verbose]
+ command = @command.join(" ")
+ system(command)
+ raise "Command failed: #{command}" unless $?.success?
+
+ @command = []
+ end
+end
+
+ok_methods = "uclust,usearch,usearch_uclust"
+
+casts = []
+casts << {:long=>'no_sort', :short=>'n', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'method', :short=>'m', :type=>'string', :mandatory=>true, :default=>"uclust", :allowed=>ok_methods, :disallowed=>nil}
+casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'comp', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'identity', :short=>'i', :type=>'float', :mandatory=>true, :default=>0.9, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'e_val', :short=>'e', :type=>'float', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+# At high identities, around 96% and above, compressed indexes are often more sensitive, faster
+# and use less RAM. Compressed indexes are disabled by default, so I generally recommend that
+# you specify the --slots and --w options when clustering at high identities.
+
+tmpdir = Biopieces.mktmpdir
+infile = File.join(tmpdir, "in.fna")
+outfile = File.join(tmpdir, "out.uc")
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ Fasta.open(infile, mode="w") do |fasta_io|
+ input.each_record do |record|
+ output.puts record
+
+ if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+ fasta_io.puts Seq.new_bp(record).to_fasta
+ end
+ end
+ end
+
+ uclust = Uclust.new(infile, outfile, options)
+ uclust.sort unless options[:no_sort] or options[:method] == "usearch"
+
+ case options[:method].to_s
+ when "uclust" then uclust.cluster
+ when "usearch" then uclust.usearch
+ when "usearch_uclust" then uclust.usearch_uclust
+ end
+
+ uclust.each do |record|
+ output.puts record
+ end
+end