From e6bec636d42b4448993fb806430e668ec5e98a53 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 27 Nov 2012 07:21:04 +0000
Subject: [PATCH] added -c to plot_nuc_dist

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2003 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_scripts/QA_454_report.rb | 24 +++++++++++++++---------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/bp_scripts/QA_454_report.rb b/bp_scripts/QA_454_report.rb
index 362c728..8c079f3 100755
--- a/bp_scripts/QA_454_report.rb
+++ b/bp_scripts/QA_454_report.rb
@@ -107,7 +107,7 @@ class Report
   end
 
   class PlotData
-    attr_reader :lendist_unclipped, :lendist_clipped, :scores_unclipped, :scores_clipped, :mean_scores, :nucleotide_dist
+    attr_reader :lendist_unclipped, :lendist_clipped, :scores_unclipped, :scores_clipped, :mean_scores, :nucleotide_dist500, :nucleotide_dist50
 
     def initialize(sff_file, tmpdir)
       @sff_file = sff_file
@@ -117,15 +117,17 @@ class Report
       @plot4    = File.join(tmpdir, "plot4.png")
       @plot5    = File.join(tmpdir, "plot5.png")
       @plot6    = File.join(tmpdir, "plot6.png")
+      @plot7    = File.join(tmpdir, "plot7.png")
 
       bp_plot
 
-      @lendist_unclipped = png2base64(@plot1)
-      @lendist_clipped   = png2base64(@plot3)
-      @scores_unclipped  = png2base64(@plot2)
-      @scores_clipped    = png2base64(@plot4)
-      @mean_scores       = png2base64(@plot5)
-      @nucleotide_dist   = png2base64(@plot6)
+      @lendist_unclipped  = png2base64(@plot1)
+      @lendist_clipped    = png2base64(@plot3)
+      @scores_unclipped   = png2base64(@plot2)
+      @scores_clipped     = png2base64(@plot4)
+      @mean_scores        = png2base64(@plot5)
+      @nucleotide_dist500 = png2base64(@plot6)
+      @nucleotide_dist50  = png2base64(@plot7)
     end
 
     def bp_plot
@@ -141,8 +143,10 @@ class Report
          mean_scores |
          bin_vals -k SCORES_MEAN -b 5 |
          plot_histogram -s num -k SCORES_MEAN_BIN -T 'Mean score bins' -X 'Bins (size 5)' -Y 'Count' -t png -o #{@plot5} |
+         extract_seq -l 500 |
+         plot_nucleotide_distribution -c -t png -o #{@plot6} |
          extract_seq -l 50 |
-         plot_nucleotide_distribution -t png -o #{@plot6} -x"
+         plot_nucleotide_distribution -t png -o #{@plot7} -x"
       )
       STDERR.puts "done.\n"
     end
@@ -306,7 +310,9 @@ template = %{
       </table>
       <h2>Residue frequency analysis</h2>
       <p>Plot of nucleotide distribution in percent of the first 50 bases:</p>
-      <p><img alt="plot_nucleotide_distribution" src="<%= @plots.nucleotide_dist %>" width="600" /></p>
+      <p><img alt="plot_nucleotide_distribution" src="<%= @plots.nucleotide_dist50 %>" width="600" /></p>
+      <p>Plot of nucleotide distribution in percent of the first 500 bases:</p>
+      <p><img alt="plot_nucleotide_distribution" src="<%= @plots.nucleotide_dist500 %>" width="600" /></p>
     </body>
   </html>
 }.gsub(/^\s+/, '')
-- 
2.39.2