#!/usr/bin/env ruby

# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# 

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


require 'biopieces'
require 'fasta'

class Uclust
  include Enumerable

  def initialize(infile, outfile)
    @infile  = infile
    @outfile = outfile
  end

  # Method that calls Uclusts sorting for sorting a FASTA file
  # according to decending sequence length.
  def sort(options)
    command = "nice -n 19"
    command << " uclust --sort #{@infile} --output #{@infile}.sort"
    command << " > /dev/null 2>&1" unless options[:verbose]
    system(command)
    raise "Failed sorting file: #{@infile}" unless $?.success?

    File.rename "#{@infile}.sort", @infile
  end

  def ublast(options)
    # uclust --ublast query_seqs.fasta --db database.fasta --blast6out filename --evalue E
    options[:e_val] = 10 if options[:e_val].is_nil?
    command = "nice -n 19"
    command << " uclust --ublast #{@infile} --db #{options[:database]} --uc #{@outfile} --evalue #{options[:e_val]}"
    command << " > /dev/null 2>&1" unless options[:verbose]
    system(command)
    raise "Command failed: #{command}" unless $?.success?
  end

  def usearch(options)
    # uclust --query query.fasta --db db.fasta --uc results.uc --id 0.90 [--evalue E]
    command = "nice -n 19"
    command << " uclust --query #{@infile} --db #{options[:database]} --uc #{@outfile} --id #{options[:identity]}"
    command << " --evalue #{options[:e_val]}" if options.has_key? :e_val
    command << " > /dev/null 2>&1" unless options[:verbose]
    system(command)
    raise "Command failed: #{command}" unless $?.success?
  end

  def uclust(options)
    # uclust --input seqs_sorted.fasta --uc results.uc --id 0.90
    command = "nice -n 19"
    command << " uclust --input #{@infile} --uc #{@outfile} --id #{options[:identity]}"
    command << " > /dev/null 2>&1" unless options[:verbose]
    system(command)
    raise "Command failed: #{command}" unless $?.success?
  end

  def usearch_uclust(options)
    # uclust --input seqs_sorted.fasta --lib db.fasta --uc results.uc --id 0.90
    command = "nice -n 19"
    command << " uclust --input #{@infile} --lib #{options[:database]} --uc #{@outfile} --id #{options[:identity]}"
    command << " --lib #{options[:database]}" if options.has_key? :database
    command << " > /dev/null 2>&1" unless options[:verbose]
    system(command)
    raise "Command failed: #{command}" unless $?.success?
  end

  def each
    record = {}

    File.open(@outfile, mode="r") do |ios|
      ios.each_line do |line|
        if line !~ /^#/
          fields = line.split("\t")

          record[:REC_TYPE] = "UCLUST"
          record[:TYPE]     = fields[0]
          record[:CLUSTER]  = fields[1]
          record[:SEQ_LEN]  = fields[2]
          record[:IDENT]    = fields[3]
          record[:STRAND]   = fields[4]
          record[:Q_BEG]    = fields[5]
          record[:S_BEG]    = fields[6]
          record[:CIGAR]    = fields[7]
          record[:Q_ID]     = fields[8]
          record[:S_ID]     = fields[9]

          yield record
        end
      end
    end

    self # conventionally
  end
end

ok_methods = "ublast,usearch,uclust,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=>'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}

bp = Biopieces.new

options = bp.parse(ARGV, casts)

tmpdir  = bp.mktmpdir
infile  = "#{tmpdir}/in.fna"
outfile = "#{tmpdir}/out.uc"

Fasta.open(infile, mode="w") do |fasta_io|
  bp.each_record do |record|
    bp.puts record
    fasta_io.puts record
  end
end

uclust = Uclust.new(infile, outfile)
uclust.sort(options) unless options[:no_sort]

case options[:method].to_s
when "ublast"         then uclust.ublast(options)
when "usearch"        then uclust.usearch(options)
when "uclust"         then uclust.uclust(options)
when "usearch_uclust" then uclust.usearch_uclust(options)  
else raise "Unknown method: #{options[:method]}"
end

uclust.each do |record|
  bp.puts record
end


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


__END__