fixed installer issue

[biopieces.git] / bp_scripts / QA_454_report.rb

diff --git a/bp_scripts/QA_454_report.rb b/bp_scripts/QA_454_report.rb
index 8c079f379ba9de4f658a88214e4ed99245d3d55f..905bfc33fef791be3e6cffde9c4388210dcaa1f8 100755 (executable)
--- a/bp_scripts/QA_454_report.rb
+++ b/bp_scripts/QA_454_report.rb
@@ -45,8 +45,7 @@ class Report
 
     def initialize(sff_file, tmpdir)
       @sff_file  = sff_file
-      @out1_file = File.join(tmpdir, "out1.txt")
-      @out2_file = File.join(tmpdir, "out2.txt")
+      @anal_file = File.join(tmpdir, "out1.txt")
       @count     = 0
       @min       = 0
       @max       = 0
@@ -58,7 +57,6 @@ class Report
 
       bp_seq_analyze
       parse_analyze_vals
-      parse_mean_vals
     end
 
     private
@@ -68,38 +66,24 @@ class Report
       system(
         "read_sff -i #{@sff_file} |
          progress_meter |
-         analyze_vals -k SEQ -o #{@out1_file} |
          analyze_seq |
-         mean_vals -k 'GC%,HARD_MASK%,SOFT_MASK%' -o #{@out2_file} -x"
+         analyze_vals -k SEQ,GC%,HARD_MASK%,SOFT_MASK% -x |
+         write_tab -o #{@anal_file} -x"
        )
       STDERR.puts "done.\n"
     end
 
     def parse_analyze_vals
-      File.open(@out1_file, "r") do |ios|
+      File.open(@anal_file, "r") do |ios|
         while not ios.eof?
-          line = ios.readline.chomp
-
-          case line
-          when /COUNT\s+(\d+)/; then @count = $1
-          when /MIN\s+(\d+)/;   then @min   = $1
-          when /MAX\s+(\d+)/;   then @max   = $1
-          when /MEAN\s+(\d+)/;  then @mean  = $1
-          when /SUM\s+(\d+)/;   then @bases = $1
-          end
-        end
-      end
-    end
-
-    def parse_mean_vals
-      File.open(@out2_file, "r") do |ios|
-        while not ios.eof?
-          line = ios.readline.chomp
-
-          case line
-          when /GC%_MEAN: (.+)/;        then @gc   = $1
-          when /HARD_MASK%_MEAN: (.+)/; then @hard = $1
-          when /SOFT_MASK%_MEAN: (.+)/; then @soft = $1
+          line   = ios.readline.chomp
+          fields = line.split("\t")
+
+          case fields.first
+          when "SEQ"        then @count, @min, @max, @bases, @mean = fields[2 .. 6]
+          when "GC%"        then @gc   = fields[6]
+          when "HARD_MASK%" then @hard = fields[6]
+          when "SOFT_MASK%" then @soft = fields[6]
           end
         end
       end