disabled inline

[biopieces.git] / code_ruby / lib / maasha / seq.rb

diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index c1ce2daed2ca8f773cb2d985afc4c04238a02939..db93dc2d37ef6aac9dd483850dd8a8a3893ad25a 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -22,9 +22,10 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'maasha/digest'
 require 'maasha/patternmatcher'
 require 'maasha/bits'
+#require 'maasha/backtrack'
+require 'maasha/digest'
 #require 'maasha/patscan'
 
 # Residue alphabets
@@ -36,6 +37,8 @@ INDELS  = %w[. - _ ~]
 # Quality scores bases
 SCORE_PHRED    = 33
 SCORE_ILLUMINA = 64
+SCORE_MIN      = 0
+SCORE_MAX      = 40
 
 # Error class for all exceptions to do with Seq.
 class SeqError < StandardError; end
@@ -43,6 +46,8 @@ class SeqError < StandardError; end
 class Seq
   #include Patscan
   include PatternMatcher
+#  include BackTrack
+  include Digest
 
   attr_accessor :seq_name, :seq, :type, :qual
 
@@ -176,8 +181,8 @@ class Seq
 
   # Method that given a Seq entry returns a FASTA entry (a string).
   def to_fasta(wrap = nil)
-    raise SeqError, "Missing seq_name" if self.seq_name.nil?
-    raise SeqError, "Missing seq"      if self.seq.nil?
+    raise SeqError, "Missing seq_name" if self.seq_name.nil? or self.seq_name == ''
+    raise SeqError, "Missing seq"      if self.seq.nil?      or self.seq.empty?
 
     seq_name = self.seq_name.to_s
     seq      = self.seq.to_s
@@ -247,9 +252,9 @@ class Seq
     raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
 
     if self.is_dna?
-      self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn' )
+      self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
     elsif self.is_rna?
-      self.seq.tr!( 'AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn' )
+      self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
     else
       raise SeqError, "Cannot complement sequence type: #{self.type}"
     end
@@ -328,22 +333,38 @@ class Seq
     self.subseq(start, length)
   end
 
-  def quality_trim(min)
-  end
-
   def quality_trim_right(min)
+    raise SeqError, "no sequence"      if self.seq.nil?
+    raise SeqError, "no quality score" if self.qual.nil?
+    raise SeqError, "minimum value: #{min} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? min
+
+    regex_right = Regexp.new("[#{(SCORE_ILLUMINA).chr}-#{(SCORE_ILLUMINA + min).chr}]+$")
+
+    self.qual.match(regex_right) do |m|
+      self.subseq!(0, $`.length) if $`.length > 0
+    end
+
+    self
   end
 
   def quality_trim_left(min)
-  end
+    raise SeqError, "no sequence"      if self.seq.nil?
+    raise SeqError, "no quality score" if self.qual.nil?
+    raise SeqError, "minimum value: #{min} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? min
 
-  def quality_trim!(min)
-  end
+    regex_left  = Regexp.new("^[#{(SCORE_ILLUMINA).chr}-#{(SCORE_ILLUMINA + min).chr}]+")
 
-  def quality_trim_right!(min)
+    self.qual.match(regex_left) do |m|
+      self.subseq!(m.to_s.length, self.length - m.to_s.length) if self.length - m.to_s.length > 0
+    end
+
+    self
   end
 
-  def quality_trim_left!(min)
+  def quality_trim(min)
+    self.quality_trim_right(min)
+    self.quality_trim_left(min)
+    self
   end
 
   # Method that returns the residue compositions of a sequence in