fixed SCORE_BASE global var

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2101 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/plot_scores b/bp_bin/plot_scores
index bf0023a6ea53c9d611a9f993f89fb1a8c721d642..30ffeb3287dcffc20e44b05dbd01f6e1543abd4b 100755 (executable)
--- a/bp_bin/plot_scores
+++ b/bp_bin/plot_scores
@@ -45,10 +45,7 @@ casts << {:long=>'ylabel',    :short=>'Y', :type=>'string', :mandatory=>false, :
 
 options = Biopieces.options_parse(ARGV, casts)
 
-ILLUMINA_BASE = 64
-ILLUMINA_MIN  = 0
-ILLUMINA_MAX  = 40
-SCORES_MAX    = 10_000
+SCORES_MAX = 10_000
 
 scores_vec = NArray.int(SCORES_MAX)
 count_vec  = NArray.int(SCORES_MAX)
@@ -62,7 +59,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
       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") - ILLUMINA_BASE
+        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
@@ -76,7 +73,7 @@ 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 *= (ILLUMINA_MAX / count_vec.max(0).to_f)
+count_vec *= (Seq::SCORE_MAX / count_vec.max(0).to_f)
 
 x  = (1 .. max).to_a
 y1 = mean_vec.to_a
@@ -90,7 +87,7 @@ Gnuplot.open do |gp|
     plot.ylabel   options[:ylabel]
     plot.output   options[:data_out] if options[:data_out]
     plot.xrange   "[#{x.min - 1}:#{x.max + 1}]"
-    plot.yrange   "[#{ILLUMINA_MIN}:#{ILLUMINA_MAX}]"
+    plot.yrange   "[#{Seq::SCORE_MIN}:#{Seq::SCORE_MAX}]"
     plot.style    "fill solid 0.5 border"
     plot.xtics    "out"
     plot.ytics    "out"

diff --git a/bp_bin/scores_to_dec b/bp_bin/scores_to_dec
index 56381a5522b023ecbde2ae9a7d3fece2aef7088c..2d91c2bda001f24767f1208d5930291fe24d014b 100755 (executable)
--- a/bp_bin/scores_to_dec
+++ b/bp_bin/scores_to_dec
@@ -28,10 +28,8 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
 require 'maasha/biopieces'
-
-ILLUMINA_BASE = 64
+require 'maasha/seq'
 
 # Expading class Hash with possibly evil monkey patch.
 class Hash
@@ -40,7 +38,7 @@ class Hash
   def scores2dec!
     if self.has_key? :SCORES
       self[:SCORES].gsub! /./ do |score|
-        score = (score.ord - ILLUMINA_BASE).to_s + ";"
+        score = (score.ord - Seq::SCORE_BASE).to_s + ";"
       end
 
       self[:SCORES].chomp! ";"

diff --git a/bp_test/test/test_find_SNPs b/bp_test/test/test_find_SNPs
index 61c570925c960531a3e4b24eb994deff0d49ef25..760e1b0be9d67d1029a194d8e520b51ec9763cca 100755 (executable)
--- a/bp_test/test/test_find_SNPs
+++ b/bp_test/test/test_find_SNPs
@@ -5,3 +5,7 @@ source "$BP_DIR/bp_test/lib/test.sh"
 run "$bp -I $in -O $tmp"
 assert_no_diff $tmp $out.1
 clean
+
+run "$bp -I $in -c -O $tmp"
+assert_no_diff $tmp $out.2
+clean

diff --git a/code_ruby/lib/maasha/align.rb b/code_ruby/lib/maasha/align.rb
index 2b63d91c3593eb93668e47e0f2ff8c0bd8824a24..ffa41c4e41e8107d4fe828ef6b81c529b320741f 100755 (executable)
--- a/code_ruby/lib/maasha/align.rb
+++ b/code_ruby/lib/maasha/align.rb
@@ -262,7 +262,7 @@ class Align
     def na_add_entries
       @entries.each_with_index do |entry, i|
         @na_seq[true, i]  = NArray.to_na(entry.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
-        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - SCORE_BASE if @has_qual
+        @na_qual[true, i] = NArray.to_na(entry.qual, "byte") - Seq::SCORE_BASE if @has_qual
       end
     end
 
@@ -375,7 +375,7 @@ class Align
 
     # Method to calculate a consensus quality from a Consensus object.
     def consensus_qual
-      (@na_qual.mean(1).round.to_type("byte") + SCORE_BASE).to_s
+      (@na_qual.mean(1).round.to_type("byte") + Seq::SCORE_BASE).to_s
     end
   end
 end

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 8833acba2f54ca3eb22407912f8421d324e6ff52..577d51a6b1d01aa96aae7170cda425638daaf21e 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -67,15 +67,16 @@ TRANS_TAB11 = {
   "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
 }
 
-# Quality scores bases
-SCORE_BASE = 64
-SCORE_MIN  = 0
-SCORE_MAX  = 40
 
 # Error class for all exceptions to do with Seq.
 class SeqError < StandardError; end
 
 class Seq
+  # Quality scores bases
+  SCORE_BASE = 64
+  SCORE_MIN  = 0
+  SCORE_MAX  = 40
+
   include Digest
   include Trim
 

diff --git a/code_ruby/lib/maasha/seq/trim.rb b/code_ruby/lib/maasha/seq/trim.rb
index a11159bd5cfd065c7f4f1a89ec540d591f01047f..8efabf9c8fe24309fdd8c3c9496e06266b1f9a91 100644 (file)
--- a/code_ruby/lib/maasha/seq/trim.rb
+++ b/code_ruby/lib/maasha/seq/trim.rb
@@ -34,7 +34,7 @@ module Trim
   def quality_trim_right(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq(0, pos)
   end
@@ -44,7 +44,7 @@ module Trim
   def quality_trim_right!(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq!(0, pos)
   end
@@ -54,7 +54,7 @@ module Trim
   def quality_trim_left(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq(pos)
   end
@@ -64,7 +64,7 @@ module Trim
   def quality_trim_left!(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     self.subseq!(pos)
   end
@@ -74,8 +74,8 @@ module Trim
   def quality_trim(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
-    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     pos_left = pos_right if pos_left > pos_right
 
@@ -87,8 +87,8 @@ module Trim
   def quality_trim!(min_qual, min_len = 1)
     check_trim_args(min_qual)
 
-    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
-    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, SCORE_BASE)
+    pos_right = trim_right_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
+    pos_left  = trim_left_pos_c(self.qual, self.length, min_qual, min_len, Seq::SCORE_BASE)
 
     pos_left = pos_right if pos_left > pos_right
 
@@ -102,8 +102,8 @@ module Trim
   def check_trim_args(min_qual)
     raise TrimError, "no sequence"      if self.seq.nil?
     raise TrimError, "no quality score" if self.qual.nil?
-    unless (SCORE_MIN .. SCORE_MAX).include? min_qual
-      raise TrimError, "minimum quality value: #{min_qual} out of range #{SCORE_MIN} .. #{SCORE_MAX}"
+    unless (Seq::SCORE_MIN .. Seq::SCORE_MAX).include? min_qual
+      raise TrimError, "minimum quality value: #{min_qual} out of range #{Seq::SCORE_MIN} .. #{Seq::SCORE_MAX}"
     end
   end