3 # Copyright (C) 2007-2011 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
21 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
23 # This program is part of the Biopieces framework (www.biopieces.org).
27 use Maasha::Biopieces;
31 # Plot a histogram of mean sequence quality scores.
33 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
40 terminals = "dumb,x11,aqua,post,pdf,png,svg"
43 casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
44 casts << {:long=>'data_out', :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
45 casts << {:long=>'terminal', :short=>'t', :type=>'string', :mandatory=>false, :default=>'dumb', :allowed=>terminals, :disallowed=>nil}
49 options = bp.parse(ARGV, casts)
53 sum_hash = Hash.new(0)
54 count_hash = Hash.new(0)
56 bp.each_record do |record|
58 scores = record[:SCORES]
59 (0 ... scores.length).each do |i|
60 sum_hash[i] += (scores[i].ord - BASE_SOLEXA)
65 bp.puts record unless options[:no_stream]
71 (0 ... sum_hash.size).each do |i|
73 y << sum_hash[i].to_f / count_hash[i].to_f
77 Gnuplot::Plot.new(gp) do |plot|
78 plot.terminal options[:terminal]
79 plot.title "Mean Quality Scores"
80 plot.ylabel "Mean score"
81 plot.xlabel "Sequence position"
82 plot.output options[:data_out] if options[:data_out]
83 plot.xrange "[#{x.min - 1}:#{x.max + 1}]"
85 plot.style "fill solid 0.5 border"
89 plot.data << Gnuplot::DataSet.new([x, y]) do |ds|
97 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<