#!/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 the nucleotide distribution in percent of sequences in the stream.

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

require 'maasha/biopieces'
require 'gnuplot'
require 'narray'
require 'pp'

VEC_MAX   = 10_000
Y_MAX     = 100

terminals = "dumb,x11,aqua,post,pdf,png,svg"
title     = "Nucleotide Distribution"
xlabel    = "Sequence position"
ylabel    = "Nucleotide distribution (%)"

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)

max_len = 0 

vec_a   = NArray.int(VEC_MAX)
vec_t   = NArray.int(VEC_MAX)
vec_c   = NArray.int(VEC_MAX)
vec_g   = NArray.int(VEC_MAX)
vec_n   = NArray.int(VEC_MAX)
vec_tot = NArray.float(VEC_MAX)

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

      unless seq.empty?
        raise BiopiecesError, "sequence too long: #{seq.length} > #{VEC_MAX}" if seq.length > VEC_MAX

        vec_seq = NArray.to_na(seq, "byte")

        vec_a[0 ... seq.length]   += vec_seq.eq('A'.ord)
        vec_t[0 ... seq.length]   += vec_seq.eq('T'.ord)
        vec_c[0 ... seq.length]   += vec_seq.eq('C'.ord)
        vec_g[0 ... seq.length]   += vec_seq.eq('G'.ord)
        vec_n[0 ... seq.length]   += vec_seq.eq('N'.ord)
        vec_tot[0 ... seq.length] += 1

        max_len = seq.length if seq.length > max_len
      end
    end

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

if max_len > 0
  x = (1 .. max_len).to_a
  a = ((vec_a / vec_tot) * 100)[0 ... max_len].to_a
  t = ((vec_t / vec_tot) * 100)[0 ... max_len].to_a
  c = ((vec_c / vec_tot) * 100)[0 ... max_len].to_a
  g = ((vec_g / vec_tot) * 100)[0 ... max_len].to_a
  n = ((vec_n / vec_tot) * 100)[0 ... max_len].to_a

  vec_tot *= (Y_MAX / vec_tot.max(0).to_f)
  y = vec_tot.to_a

  a.unshift 0.0
  t.unshift 0.0
  c.unshift 0.0
  g.unshift 0.0
  n.unshift 0.0

  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.ytics    "out"
      plot.xtics    "out"
      plot.yrange   "[0:#{Y_MAX}]"
      plot.xrange   "[0:#{max_len}]"
      plot.auto     "fix"
      plot.offsets  "1"
      plot.key      "outside right top vertical Left reverse enhanced autotitles columnhead nobox"
      plot.key      "invert samplen 4 spacing 1 width 0 height 0"
      plot.style    "fill solid 0.5 border"
      plot.style    "histogram rowstacked"
      plot.style    "data histograms"
      plot.boxwidth "0.75 absolute"

      plot.data << Gnuplot::DataSet.new(n) do |ds|
        ds.using = "1"
        ds.with  = "histogram lt rgb \"black\""
        ds.title = "N"
      end

      plot.data << Gnuplot::DataSet.new(g) do |ds|
        ds.using = "1"
        ds.with  = "histogram lt rgb \"yellow\""
        ds.title = "G"
      end

      plot.data << Gnuplot::DataSet.new(c) do |ds|
        ds.using = "1"
        ds.with  = "histogram lt rgb \"blue\""
        ds.title = "C"
      end

      plot.data << Gnuplot::DataSet.new(t) do |ds|
        ds.using = "1"
        ds.with  = "histogram lt rgb \"green\""
        ds.title = "T"
      end

      plot.data << Gnuplot::DataSet.new(a) do |ds|
        ds.using = "1"
        ds.with  = "histogram lt rgb \"red\""
        ds.title = "A"
      end

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

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


__END__