#!/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).

use warnings;
use strict;
use Maasha::Biopieces;
use Maasha::Fastq;
use Maasha::Plot;

# Plot a histogram of mean sequence quality scores.

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


require 'biopieces'
require 'gnuplot'
require 'pp'

terminals = "dumb,x11,aqua,post,pdf,png,svg"

casts = []
casts << {:long=>'no_stream', :short=>'x', :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}

bp = Biopieces.new

options = bp.parse(ARGV, casts)

BASE_SOLEXA = 64

sum_hash   = Hash.new(0)
count_hash = Hash.new(0)

bp.each_record do |record|
  if record[:SCORES]
    scores = record[:SCORES]
    (0 ... scores.length).each do |i|
      sum_hash[i]   += (scores[i].ord - BASE_SOLEXA)
      count_hash[i] += 1
    end
  end

  bp.puts record unless options[:no_stream]
end

x = []
y = []

(0 ... sum_hash.size).each do |i|
  x << i
  y << sum_hash[i].to_f / count_hash[i].to_f
end

Gnuplot.open do |gp|
  Gnuplot::Plot.new(gp) do |plot|
    plot.terminal options[:terminal]
    plot.title    "Mean Quality Scores"
    plot.ylabel   "Mean score"
    plot.xlabel   "Sequence position"
    plot.output   options[:data_out] if options[:data_out]
    plot.xrange   "[#{x.min - 1}:#{x.max + 1}]"
    plot.yrange   "[0:40]"
    plot.style    "fill solid 0.5 border"
    plot.xtics    "out"
    plot.ytics    "out"
    
    plot.data << Gnuplot::DataSet.new([x, y]) do |ds|
      ds.with = "boxes"
      ds.notitle
    end
  end
end


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


__END__