3 # Copyright (C) 2007-2012 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 # Plot a histogram of mean sequence quality scores.
25 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
27 require 'maasha/biopieces'
32 terminals = "dumb,x11,aqua,post,pdf,png,svg"
33 title = "Mean Quality Scores"
34 xlabel = "Sequence position"
38 casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
39 casts << {:long=>'count', :short=>'c', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
40 casts << {:long=>'data_out', :short=>'o', :type=>'file', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
41 casts << {:long=>'terminal', :short=>'t', :type=>'string', :mandatory=>false, :default=>'dumb', :allowed=>terminals, :disallowed=>nil}
42 casts << {:long=>'title', :short=>'T', :type=>'string', :mandatory=>false, :default=>title, :allowed=>nil, :disallowed=>nil}
43 casts << {:long=>'xlabel', :short=>'X', :type=>'string', :mandatory=>false, :default=>xlabel, :allowed=>nil, :disallowed=>nil}
44 casts << {:long=>'ylabel', :short=>'Y', :type=>'string', :mandatory=>false, :default=>ylabel, :allowed=>nil, :disallowed=>nil}
46 options = Biopieces.options_parse(ARGV, casts)
53 scores_vec = NArray.int(SCORES_MAX)
54 count_vec = NArray.int(SCORES_MAX)
57 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
58 input.each_record do |record|
60 scores = record[:SCORES]
63 raise BiopiecesError, "score string too long: #{scores.length} > #{SCORES_MAX}" if scores.length > SCORES_MAX
65 scores_vec[0 ... scores.length] += NArray.to_na(scores, "byte") - ILLUMINA_BASE
66 count_vec[0 ... scores.length] += 1
68 max = scores.length if scores.length > max
72 output.puts record unless options[:no_stream]
76 mean_vec = NArray.sfloat(max)
77 mean_vec = scores_vec[0 ... max].to_f / count_vec[0 ... max]
78 count_vec = count_vec[0 ... max].to_f
79 count_vec *= (ILLUMINA_MAX / count_vec.max(0).to_f)
86 Gnuplot::Plot.new(gp) do |plot|
87 plot.terminal options[:terminal]
88 plot.title options[:title]
89 plot.xlabel options[:xlabel]
90 plot.ylabel options[:ylabel]
91 plot.output options[:data_out] if options[:data_out]
92 plot.xrange "[#{x.min - 1}:#{x.max + 1}]"
93 plot.yrange "[#{ILLUMINA_MIN}:#{ILLUMINA_MAX}]"
94 plot.style "fill solid 0.5 border"
98 plot.data << Gnuplot::DataSet.new([x, y1]) do |ds|
100 ds.title = "mean score"
104 plot.data << Gnuplot::DataSet.new([x, y2]) do |ds|
105 ds.with = "lines lt rgb \"black\""
106 ds.title = "relative count"
113 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<