#!/usr/bin/env ruby

# Copyright (C) 2007-2011 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 program is part of the Biopieces framework (www.biopieces.org).

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# Run Uclust on sequences in the stream.

# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

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


# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<


__END__