# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
require 'maasha/bits'
-require 'maasha/seq/backtrack'
require 'maasha/seq/digest'
-#require 'maasha/seq/patscan'
-require 'maasha/seq/patternmatcher'
require 'maasha/seq/trim'
require 'narray'
+autoload :BackTrack, 'maasha/seq/backtrack.rb'
+autoload :Dynamic, 'maasha/seq/dynamic.rb'
+
# Residue alphabets
DNA = %w[a t c g]
RNA = %w[a u c g]
class SeqError < StandardError; end
class Seq
- #include Patscan
- include PatternMatcher
- include BackTrack
include Digest
include Trim
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
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
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