From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Fri, 21 Sep 2012 09:10:48 +0000 (+0000)
Subject: added qual_base(33|64)? methods to seq.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=ef58435aaed269612750b6c40c3a7b05efcc5df0;p=biopieces.git

added qual_base(33|64)? methods to seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1936 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index d13cdab..a864601 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -538,8 +538,21 @@ class Seq
     self
   end
 
+  # Method that determines if a quality score string can be
+  # absolutely identified as base 33.
+  def qual_base33?
+    self.qual.match(/[!-:]/)
+  end
+
+  # Method that determines if a quality score string can be
+  # absolutely identified as base 64.
+  def qual_base64?
+    self.qual.match(/[K-h]/)
+  end
+
   # Method to convert quality scores inbetween formats.
   # Sanger     base 33, range  0-40 
+  # 454        base 64, range  0-40 
   # Solexa     base 64, range -5-40 
   # Illumina13 base 64, range  0-40 
   # Illumina15 base 64, range  3-40 
@@ -550,6 +563,7 @@ class Seq
 
       case from.downcase
       when "sanger"     then na_qual -= 33
+      when "454"        then na_qual -= 64
       when "solexa"     then na_qual -= 64
       when "illumina13" then na_qual -= 64
       when "illumina15" then na_qual -= 64
@@ -559,6 +573,7 @@ class Seq
 
       case to.downcase
       when "sanger"     then na_qual += 33
+      when "454"        then na_qual += 64
       when "solexa"     then na_qual += 64
       when "illumina13" then na_qual += 64
       when "illumina15" then na_qual += 64