#!/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

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

# Plot a histogram of mean sequence quality scores.

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

require 'maasha/biopieces'
require 'maasha/seq'
require 'gnuplot'
require 'narray'

terminals = "dumb,x11,aqua,post,pdf,png,svg"
title     = "Mean Quality Scores"
xlabel    = "Sequence position"
ylabel    = "Mean score"

casts = []
casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil,    :allowed=>nil,       :disallowed=>nil}
casts << {:long=>'count',     :short=>'c', :type=>'flag',   :mandatory=>false, :default=>nil,    :allowed=>nil,       :disallowed=>nil}
casts << {:long=>'data_out',  :short=>'o', :type=>'file',   :mandatory=>false, :default=>nil,    :allowed=>nil,       :disallowed=>nil}
casts << {:long=>'terminal',  :short=>'t', :type=>'string', :mandatory=>false, :default=>'dumb', :allowed=>terminals, :disallowed=>nil}
casts << {:long=>'title',     :short=>'T', :type=>'string', :mandatory=>false, :default=>title,  :allowed=>nil,       :disallowed=>nil}
casts << {:long=>'xlabel',    :short=>'X', :type=>'string', :mandatory=>false, :default=>xlabel, :allowed=>nil,       :disallowed=>nil}
casts << {:long=>'ylabel',    :short=>'Y', :type=>'string', :mandatory=>false, :default=>ylabel, :allowed=>nil,       :disallowed=>nil}

options = Biopieces.options_parse(ARGV, casts)

SCORES_MAX = 10_000

scores_vec = NArray.int(SCORES_MAX)
count_vec  = NArray.int(SCORES_MAX)
max        = 0

Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
  input.each_record do |record|
    if record[:SCORES]
      scores = record[:SCORES]

      if scores.length > 0
        raise BiopiecesError, "score string too long: #{scores.length} > #{SCORES_MAX}" if scores.length > SCORES_MAX

        scores_vec[0 ... scores.length] += NArray.to_na(scores, "byte") - Seq::SCORE_BASE
        count_vec[0 ... scores.length]  += 1

        max = scores.length if scores.length > max
      end
    end

    output.puts record unless options[:no_stream]
  end
end

mean_vec   = NArray.sfloat(max)
mean_vec   = scores_vec[0 ... max].to_f / count_vec[0 ... max]
count_vec  = count_vec[0 ... max].to_f
count_vec *= (Seq::SCORE_MAX / count_vec.max(0).to_f)

x  = (1 .. max).to_a
y1 = mean_vec.to_a
y2 = count_vec.to_a

Gnuplot.open do |gp|
  Gnuplot::Plot.new(gp) do |plot|
    plot.terminal options[:terminal]
    plot.title    options[:title]
    plot.xlabel   options[:xlabel]
    plot.ylabel   options[:ylabel]
    plot.output   options[:data_out] if options[:data_out]
    plot.xrange   "[#{x.min - 1}:#{x.max + 1}]"
    plot.yrange   "[#{Seq::SCORE_MIN}:#{Seq::SCORE_MAX}]"
    plot.style    "fill solid 0.5 border"
    plot.xtics    "out"
    plot.ytics    "out"
    
    plot.data << Gnuplot::DataSet.new([x, y1]) do |ds|
      ds.with  = "boxes"
      ds.title = "mean score"
    end

    if options[:count]
      plot.data << Gnuplot::DataSet.new([x, y2]) do |ds|
        ds.with  = "lines lt rgb \"black\""
        ds.title = "relative count"
      end
    end
  end
end


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


__END__