--- /dev/null
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2013 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 'pp'
+
+terminals = "dumb,x11,aqua,post,pdf,png,svg"
+title = "Stacked Histogram"
+
+casts = []
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cols', :short=>'c', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'rows', :short=>'r', :type=>'string', :mandatory=>true, :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=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'ylabel', :short=>'Y', :type=>'string', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+class PlotData
+ include Enumerable
+
+ def initialize()
+ @data = Hash.new { |h, k| h[k] = Hash.new(0) }
+ @seen_cols = {}
+ @seen_rows = {}
+ @table = []
+ end
+
+ def add(row, col)
+ @data[col][row] += 1
+ @seen_cols[col] = true
+ @seen_rows[row] = true
+ end
+
+ def each
+ tabulize() if @table.empty?
+
+ @table.each do |row|
+ yield row
+ end
+ end
+
+ def row_titles(i)
+ @seen_rows.keys[i]
+ end
+
+ def col_titles
+ titles = []
+
+ @seen_cols.keys.each_with_index do |col, i|
+ titles << %{"#{col}" #{i}}
+ end
+
+ "(" + titles.join(", ") + ")"
+ end
+
+ private
+
+ def tabulize
+ @seen_rows.size.times { @table << Array.new(@seen_cols.size, 0) } # table init
+
+ i = 0
+
+ @seen_cols.each_key do |col|
+ j = 0
+
+ @seen_rows.each_key do |row|
+ @table[j][i] = @data[col][row]
+
+ j += 1
+ end
+
+ i += 1
+ end
+
+ @table
+ end
+end
+
+data = PlotData.new()
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ cols = record[options[:cols].to_sym]
+ rows = record[options[:rows].to_sym]
+
+ if cols and rows
+ data.add(rows, cols)
+ end
+
+ output.puts record unless options[:no_stream]
+ end
+end
+
+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.yrange "[0:100]"
+# 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.xtics "out"
+ plot.xtics "norangelimit"
+ plot.xtics data.col_titles
+
+ data.each_with_index do |row, i|
+ plot.data << Gnuplot::DataSet.new(row.unshift(0)) do |ds|
+ ds.using = "1:xtic(2)"
+ ds.title = data.row_titles(i)
+ end
+ end
+ end
+end
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__