From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 2 May 2011 13:41:55 +0000 (+0000)
Subject: ported plot_scores to ruby
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=c99b48ef600e53e67be86bd408a9efbd3204859b;p=biopieces.git

ported plot_scores to ruby

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1352 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/plot_scores b/bp_bin/plot_scores
index 6b1360e..af37cc2 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) 2007-2011 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
@@ -18,13 +18,9 @@
 
 # http://www.gnu.org/copyleft/gpl.html
 
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Create a lineplot from quality scores in the stream.
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# This program is part of the Biopieces framework (www.biopieces.org).
 
 use warnings;
 use strict;
@@ -32,74 +28,70 @@ use Maasha::Biopieces;
 use Maasha::Fastq;
 use Maasha::Plot;
 
+# Plot a histogram of mean sequence quality scores.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $default, $terminals, $record, %count_hash, %sum_hash, $i, @scores, @data_list, $result, $fh, $tmp_dir );
-
-$default   = "Quality Scores";
-$terminals = "dumb,x11,aqua,post,svg";
-
-$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 => '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' } )
-    {
-        for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
-        {
-            $count_hash{ $i }++;
-            $sum_hash{ $i } += Maasha::Fastq::solexa2dec( substr $record->{ "SCORES" }, $i, 1 );
-        }
-    }
-
-    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 'biopieces'
+require 'gnuplot'
+require 'pp'
+
+terminals = "dumb,x11,aqua,post,pdf,png,svg"
+
+casts = []
+casts << {:long=>'no_stream', :short=>'x', :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}
+
+bp = Biopieces.new
+
+options = bp.parse(ARGV, casts)
+
+BASE_SOLEXA = 64
+
+sum_hash   = Hash.new(0)
+count_hash = Hash.new(0)
+
+bp.each_record do |record|
+  if record[:SCORES]
+    scores = record[:SCORES]
+    (0 ... scores.length).each do |i|
+      sum_hash[i]   += (scores[i].ord - BASE_SOLEXA)
+      count_hash[i] += 1
+    end
+  end
+
+  bp.puts record unless options[:no_stream]
+end
+
+x = []
+y = []
+
+(0 ... sum_hash.size).each do |i|
+  x << i
+  y << sum_hash[i].to_f / count_hash[i].to_f
+end
+
+Gnuplot.open do |gp|
+  Gnuplot::Plot.new(gp) do |plot|
+    plot.terminal options[:terminal]
+    plot.title    "Mean Quality Scores"
+    plot.ylabel   "Mean score"
+    plot.xlabel   "Sequence position"
+    plot.output   options[:data_out] if options[:data_out]
+    plot.xrange   "[#{x.min - 1}:#{x.max + 1}]"
+    plot.yrange   "[0:40]"
+    plot.style    "fill solid 0.5 border"
+    plot.xtics    "out"
+    plot.ytics    "out"
+    
+    plot.data << Gnuplot::DataSet.new([x, y]) do |ds|
+      ds.with = "boxes"
+      ds.notitle
+    end
+  end
+end
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<