seq.rb in bio-1.1.0

- old
+ new

@@ -1,13 +1,13 @@
 #
 # = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
 #
 # Copyright::   Copyright (C) 2005
 #               Toshiaki Katayama <k@bioruby.org>
-# License::     Ruby's
+# License::     The Ruby License
 #
-# $Id: seq.rb,v 1.17 2006/02/09 20:48:53 k Exp $
+# $Id: seq.rb,v 1.21 2007/04/05 23:35:41 trevor Exp $
 #
 
 module Bio::Shell
 
   private
@@ -15,11 +15,11 @@
   # Convert sequence to colored HTML string
   def htmlseq(str)
     if str.kind_of?(Bio::Sequence)
       seq = str
     else
-      seq = seq(str)
+      seq = getseq(str)
     end
 
     if seq.is_a?(Bio::Sequence::AA)
       scheme = Bio::ColorScheme::Taylor
     else
@@ -39,16 +39,25 @@
     html += "</div>\n"
     return html
   end
 
 
+  def sixtrans(str)
+    seq = getseq(str)
+    [ 1, 2, 3, -1, -2, -3 ].each do |frame|
+      title = "Translation #{frame.to_s.rjust(2)}"
+      puts seq.translate(frame).to_fasta(title, 60)
+    end
+  end
+
+
   # Displays some basic properties of the sequence.
   def seqstat(str)
     max = 150
-    seq = seq(str)
+    seq = getseq(str)
     rep = "\n* * * Sequence statistics * * *\n\n"
-    if seq.respond_to?(:complement)
+    if seq.moltype == Bio::Sequence::NA
       fwd = seq
       rev = seq.complement
       if seq.length > max
         dot = " ..."
         fwd = fwd.subseq(1, max)
@@ -121,16 +130,16 @@
   end
 
   # Displays a DNA sequence by ascii art in B-type double helix.
   # Argument need to be at least 16 bases in length.
   def doublehelix(str)
-    seq = seq(str)
-    if str.length < 16
+    seq = getseq(str)
+    if seq.length < 16
       warn "Error: Sequence must be longer than 16 bases."
       return
     end
-    if ! seq.respond_to?(:complement)
+    if seq.moltype != Bio::Sequence::NA
       warn "Error: Sequence must be a DNA sequence."
       return
     end
     pairs = [ [5, 0], [4, 2], [3, 3], [2, 4], 
               [1, 4], [0, 3], [0, 2], [1, 0] ]
@@ -148,9 +157,27 @@
 
 end
 
 
 class String
+
+  def step(window_size)
+    i = 0
+    0.step(self.length - window_size, window_size) do |i|
+      yield self[i, window_size]
+    end
+    yield self[i + window_size .. -1] if i + window_size < self.length
+  end
+
+  def skip(window_size, step_size = 1)
+    i = 0
+    0.step(self.length - window_size, step_size) do |i|
+      yield [self[i, window_size], i + 1, i + window_size]
+    end
+    from = i + step_size
+    to  = [self.length, i + step_size + window_size].min
+    yield [self[from, window_size], from + 1, to] if from + 1 <= to
+  end
 
   def to_naseq
     Bio::Sequence::NA.new(self)
   end
 