#!/usr/bin/env ruby

# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

# HMMER search sequences in the stream against a specified database.

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

require 'pp'
require 'maasha/biopieces'
require 'maasha/fasta'

class Hash
  def to_bp
    record         = self
    bp             = {}
    bp[:REC_TYPE]  = "HMMER" 
    bp[:S_ID]      = record[:target_name]
    bp[:S_AC]      = record[:target_accession]
    bp[:Q_ID]      = record[:query_name]
    bp[:Q_AC]      = record[:query_accession]
    bp[:E_VAL_SEQ] = record[:e_value_sequence]
    bp[:SCORE_SEQ] = record[:score_sequence]
    bp[:BIAS_SEQ]  = record[:bias_sequence]
    bp[:E_VAL_DOM] = record[:e_value_domain]
    bp[:SCORE_DOM] = record[:score_domain]
    bp[:BIAS_DOM]  = record[:bias_domain]
    bp[:EXP]       = record[:exp]
    bp[:REG]       = record[:reg]
    bp[:CLU]       = record[:clu]
    bp[:OV]        = record[:ov]
    bp[:ENV]       = record[:env]
    bp[:DOM]       = record[:dom]
    bp[:REP]       = record[:rep]
    bp[:INC]       = record[:inc]
    bp[:DESC]      = record[:description_of_target]

    bp
  end
end

class Hmmer
  def initialize(output_file, options)
    @output_file = output_file
    @options     = options
    @command     = []
  end

  def search_db(query_file)
    @command << "hmmsearch"
    @command << "--tblout #{@output_file}"
    @command << "--cpu #{@options[:cpus]}"
    @command << @options[:database]
    @command << query_file

    execute
  end

  def each
    records = []

    File.open(@output_file, "r") do |ios|

      # target name    accession  query name           accession    E-value  score  bias   E-value  score  bias   exp reg
      # clu  ov env dom rep inc description of target
      ios.each_line do |line|
        next if line[0] == '#'
        fields = line.chomp.split(" ")

        record = {}
        record[:target_name]           = fields[0]
        record[:target_accession]      = fields[1]
        record[:query_name]            = fields[2]
        record[:query_accession]       = fields[3]
        record[:e_value_sequence]      = fields[4].to_f
        record[:score_sequence]        = fields[5].to_f
        record[:bias_sequence]         = fields[6].to_f
        record[:e_value_domain]        = fields[7].to_f
        record[:score_domain]          = fields[8].to_f
        record[:bias_domain]           = fields[9].to_f
        record[:exp]                   = fields[10].to_f
        record[:reg]                   = fields[11].to_i
        record[:clu]                   = fields[12].to_i
        record[:ov]                    = fields[13].to_i
        record[:env]                   = fields[14].to_i
        record[:dom]                   = fields[15].to_i
        record[:rep]                   = fields[16].to_i
        record[:inc]                   = fields[17].to_i
        record[:description_of_target] = fields[18]

        if block_given?
          yield record
        else
          records << record
        end
      end
    end

    return records if block_given?
  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 << "> /dev/null 2>&1" unless @options[:verbose]

    command = @command.join(" ")
    $stderr.puts "Running command: #{command}" if @options[:verbose]
    system(command)
    raise "Command failed: #{command}" unless $?.success?

    @command = []
  end
end

casts = []
casts << {:long=>'database', :short=>'d', :type=>'file!', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'cpus',     :short=>'c', :type=>'uint',  :mandatory=>false, :default=>1,   :allowed=>nil, :disallowed=>"0"}

options     = Biopieces.options_parse(ARGV, casts)
tmpdir      = Biopieces.mktmpdir
output_file = File.join(tmpdir, "output.tab")
query_file  = File.join(tmpdir, "query.fna")

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  Fasta.open(query_file, "w") do |fasta_io|
    input.each_record do |record|
      if record[:SEQ_NAME] and record[:SEQ]
        entry = Seq.new_bp(record)

        fasta_io.puts entry.to_fasta
      end

      output.puts record
    end
  end

  hm = Hmmer.new(output_file, options)
  hm.search_db(query_file)

  hm.each do |hit|
    output.puts hit.to_bp
  end
end

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


__END__