X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fplot_scores;h=8cc276d2f0e81055e2641bda2c0f683e183b4f94;hb=a2f82dca77855723ddc50dfb6a763da8558b7610;hp=bfe87ccacd6fba8da2f24436665ca4d7382d4b75;hpb=f72fb3b8d2883afdb21efd27d16412b7211883d9;p=biopieces.git

diff --git a/bp_bin/plot_scores b/bp_bin/plot_scores
index bfe87cc..8cc276d 100755
--- a/bp_bin/plot_scores
+++ b/bp_bin/plot_scores
@@ -1,6 +1,6 @@
-#!/usr/bin/env perl
+#!/usr/bin/env ruby
 
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# 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
@@ -18,112 +18,93 @@
 
 # http://www.gnu.org/copyleft/gpl.html
 
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Create a lineplot from quality scores in the stream.
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Fastq;
-use Maasha::Plot;
-use Maasha::Calc;
-
+# Plot a histogram of mean sequence quality scores.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
-my ( $options, $in, $out, $default, $terminals, $formats, $record, %count_hash, %sum_hash, $i, @scores, @data_list, $result, $fh, $tmp_dir );
-
-$default   = "Quality Scores";
-$terminals = "dumb,x11,aqua,post,svg";
-$formats   = "solexa,phred,decimal";
-
-$options = Maasha::Biopieces::parse_options(
-    [
-        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'data_out',   short => 'o', type => 'file',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'format'  ,   short => 'f', type => 'string', mandatory => 'no',  default => "solexa", allowed => $formats,   disallowed => undef },
-        { long => 'terminal',   short => 't', type => 'string', mandatory => 'no',  default => 'dumb',   allowed => $terminals, disallowed => undef },
-        { long => 'title',      short => 'T', type => 'string', mandatory => 'no',  default => $default, allowed => undef,      disallowed => undef },
-        { long => 'xlabel',     short => 'X', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'ylabel',     short => 'Y', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-    ]   
-);
-
-$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-{
-    if ( $record->{ 'SCORES' } )
-    {
-        if ( $options->{ 'format' } eq "solexa" )
-        {
-            for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
-            {
-                $count_hash{ $i }++;
-                $sum_hash{ $i } += Maasha::Fastq::solexa2dec( substr $record->{ "SCORES" }, $i, 1 );
-            }
-        }
-        elsif ( $options->{ 'format' } eq "phred" )
-        {
-            for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
-            {
-                $count_hash{ $i }++;
-                $sum_hash{ $i } += Maasha::Fastq::phred2dec( substr $record->{ "SCORES" }, $i, 1 );
-            }
-        }
-        else
-        {
-            @scores = split ";", $record->{ 'SCORES' };
-
-            for ( $i = 0; $i < @scores; $i++ )
-            {
-                $count_hash{ $i }++;
-                $sum_hash{ $i } += $scores[ $i ];
-            }
-        }
-    }
-
-    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-}
-
-for ( $i = 0; $i < keys %count_hash; $i++ ) {
-    push @data_list, [ $sum_hash{ $i } / $count_hash{ $i } ];
-}
-
-$tmp_dir = Maasha::Biopieces::get_tmpdir();
-
-$result = Maasha::Plot::lineplot_simple( \@data_list, $options, $tmp_dir );
-
-$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
-
-print $fh "$_\n" foreach @{ $result };
-
-close $fh;
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
-
-
-END
-{
-    Maasha::Biopieces::status_log();
-}
+require 'maasha/biopieces'
+require 'maasha/seq'
+require 'gnuplot'
+require 'narray'
+
+terminals = "dumb,x11,aqua,post,pdf,png,svg"
+title     = "Mean Quality Scores"
+xlabel    = "Sequence position"
+ylabel    = "Mean score"
+
+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)
+
+SCORES_MAX = 100_000
+
+scores_vec = NArray.int(SCORES_MAX)
+count_vec  = NArray.int(SCORES_MAX)
+max        = 0
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    if record[:SCORES]
+      scores = record[:SCORES]
+
+      if scores.length > 0
+        raise BiopiecesError, "score string too long: #{scores.length} > #{SCORES_MAX}" if scores.length > SCORES_MAX
+
+        scores_vec[0 ... scores.length] += NArray.to_na(scores, "byte") - Seq::SCORE_BASE
+        count_vec[0 ... scores.length]  += 1
+
+        max = scores.length if scores.length > max
+      end
+    end
+
+    output.puts record unless options[:no_stream]
+  end
+end
+
+mean_vec   = NArray.sfloat(max)
+mean_vec   = scores_vec[0 ... max].to_f / count_vec[0 ... max]
+count_vec  = count_vec[0 ... max].to_f
+count_vec *= (Seq::SCORE_MAX / count_vec.max(0).to_f)
+
+x  = (1 .. max).to_a
+y1 = mean_vec.to_a
+y2 = count_vec.to_a
+
+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.xrange   "[#{x.min - 1}:#{x.max + 1}]"
+    plot.yrange   "[#{Seq::SCORE_MIN}:#{Seq::SCORE_MAX}]"
+    plot.style    "fill solid 0.5 border"
+    plot.xtics    "out"
+    plot.ytics    "out"
+    
+    plot.data << Gnuplot::DataSet.new([x, y1]) do |ds|
+      ds.with  = "boxes"
+      ds.title = "mean score"
+    end
+
+    if options[:count]
+      plot.data << Gnuplot::DataSet.new([x, y2]) do |ds|
+        ds.with  = "lines lt rgb \"black\""
+        ds.title = "relative count"
+      end
+    end
+  end
+end
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<