removed debug message

[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 a2d5bbac3462d44401d0e1d97a70101f1b7d3af4..7377da533d50ea34fb4dc12c3e2bfb7f05a7e944 100644 (file)
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -136,7 +136,7 @@ class Seq
     @type     = options[:type]
     @qual     = options[:qual]
 
-    if @qual and @seq.length != @qual.length
+    if @seq and @qual and @seq.length != @qual.length
       raise SeqError, "Sequence length and score length mismatch: #{@seq.length} != #{@qual.length}"
     end
   end
@@ -294,8 +294,8 @@ class Seq
     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
+    seq_name = self.seq_name
+    seq      = self.seq.dup
 
     unless wrap.nil?
       seq.gsub!(/(.{#{wrap}})/) do |match|
@@ -305,7 +305,7 @@ class Seq
       seq.chomp!
     end
 
-    ">" + seq_name + $/ + seq + $/
+    ">" + seq_name.to_s + $/ + seq + $/
   end
 
   # Method that given a Seq entry returns a FASTQ entry (a string).
@@ -343,12 +343,14 @@ class Seq
 
   # Method to reverse the sequence.
   def reverse
-    Seq.new(
+    entry = Seq.new(
       seq_name: self.seq_name,
       seq:      self.seq.reverse,
       type:     self.type,
       qual:     (self.qual ? self.qual.reverse : self.qual)
     )
+
+    entry
   end
 
   # Method to reverse the sequence.
@@ -467,7 +469,7 @@ class Seq
   # Index method for Seq objects.
   def [](*args)
     entry = Seq.new
-    entry.seq_name = self.seq_name
+    entry.seq_name = self.seq_name.dup if self.seq_name
     entry.seq      = self.seq[*args]
     entry.type     = self.type
     entry.qual     = self.qual[*args] unless self.qual.nil?
@@ -483,41 +485,6 @@ class Seq
     self
   end
 
-  # Method that returns a subsequence of from a given start position
-  # and of a given length.
-  def subseq(start, length = self.length - start)
-    raise SeqError, "subsequence start: #{start} < 0"                                                if start  < 0
-    raise SeqError, "subsequence length: #{length} < 0"                                              if length < 0
-    raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-
-    if length == 0
-      seq  = ""
-      qual = "" unless self.qual.nil?
-    else
-      stop = start + length - 1
-
-      seq  = self.seq[start .. stop]
-      qual = self.qual[start .. stop] unless self.qual.nil?
-    end
-
-    seq_name = self.seq_name.nil? ? nil : self.seq_name.dup
-
-    Seq.new(seq_name: seq_name, seq: seq, type: self.type, qual: qual)
-  end
-
-  # Method that replaces a sequence with a subsequence from a given start position
-  # and of a given length.
-  def subseq!(start, length = self.length - start)
-    s = subseq(start, length)
-
-    self.seq_name = s.seq_name
-    self.seq      = s.seq
-    self.type     = s.type
-    self.qual     = s.qual
-
-    self
-  end
-
   # Method that returns a subsequence of a given length
   # beginning at a random position.
   def subseq_rand(length)
@@ -527,7 +494,7 @@ class Seq
       start = rand(self.length - length + 1)
     end
 
-    self.subseq(start, length)
+    self[start .. start + length]
   end
 
   # Method that returns the residue compositions of a sequence in
@@ -667,22 +634,26 @@ class Seq
     regex_start = Regexp.new(start_codons.join('|'), true)
     regex_stop  = Regexp.new(stop_codons.join('|'), true)
 
-    while pos_beg and pos_beg < self.length - size_min
-      if pos_beg = self.seq.index(regex_start, pos_beg)
-        if pos_end = self.seq.index(regex_stop, pos_beg)
-          length = (pos_end - pos_beg) + 3
+    while pos_beg = self.seq.index(regex_start, pos_beg)
+      pos_end = pos_beg + 3
+       
+      while pos_end = self.seq.index(regex_stop, pos_end)
+        length = (pos_end - pos_beg) + 3
 
-          if (length % 3) == 0
-            if size_min <= length and length <= size_max
-              subseq = self.subseq(pos_beg, length)
+        if (length % 3) == 0
+          if size_min <= length and length <= size_max
+            subseq = self[pos_beg ... pos_beg + length]
 
-              orfs << [subseq, pos_beg, pos_end + 3]
-            end
+            orfs << [subseq, pos_beg, pos_end + 3]
           end
+
+          break
         end
 
-        pos_beg += 1
+        pos_end += 1
       end
+
+      pos_beg += 1
     end
 
     if pick_longest