+# Copyright (C) 2011 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/fasta'
+
+# Error class for all exceptions to do with Usearch.
+class UsearchError < StandardError; end
+
+SORT_LIMIT = 2_000_000_000 # use mergesort for files biggern than 2Gb.
+
+class Usearch
+ 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_length
+ # 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 that calls Usearch sorting for sorting a FASTA file
+ # according to cluster size.
+ def sort_size
+ # usearch -sortsize seqs.fasta -output seqs.sorted.fasta
+ @command << "usearch --sortsize #{@infile} --output #{@infile}.sort"
+
+ 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
+ @command << "usearch --query #{@infile} --db #{@options[:database]} --userout #{@outfile}"
+ @command << "--userfields target+tloz+thiz+query+bits+strand"
+ @command << "--id #{@options[:identity]}" if @options.has_key? :identity
+ @command << "--evalue #{@options[:e_val]}" if @options.has_key? :e_val
+ @command << "--rev"
+
+ execute
+ end
+
+ # Method to parse a Uclust .uc file and for each line of data
+ # yield a Biopiece record.
+ def each_cluster
+ record = {}
+
+ File.open(@outfile, mode="r") do |ios|
+ ios.each_line do |line|
+ if line !~ /^#/
+ fields = line.chomp.split("\t")
+
+ next if fields[0] == 'C'
+
+ record[:TYPE] = fields[0]
+ record[:CLUSTER] = fields[1].to_i
+ record[:IDENT] = fields[3].to_f
+ record[:Q_ID] = fields[8]
+
+ yield record
+ end
+ end
+ end
+
+ self # conventionally
+ end
+
+ # Method to parse a Useach user defined tabular file and for each line of data
+ # yield a Biopiece record.
+ def each_hit
+ record = {}
+
+ File.open(@outfile, mode="r") do |ios|
+ ios.gets # skip comment line
+ ios.each_line do |line|
+ fields = line.chomp.split("\t")
+
+ record[:REC_TYPE] = "USEARCH"
+ record[:S_ID] = fields[0]
+ record[:S_BEG] = fields[1].to_i
+ record[:S_END] = fields[2].to_i
+ record[:Q_ID] = fields[3]
+ record[:SCORE] = fields[4].to_f
+ record[:STRAND] = fields[5]
+
+ yield record
+ 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
+
+__END__
+