From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Thu, 3 Feb 2011 15:56:38 +0000 (+0000)
Subject: crude polish of shred_seq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=7bad75ba44c304fb33a5768781357b415e8c6816;p=biopieces.git

crude polish of shred_seq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1251 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/shred_seq b/bp_bin/shred_seq
index aaff5b7..6c1a8d0 100755
--- a/bp_bin/shred_seq
+++ b/bp_bin/shred_seq
@@ -50,18 +50,7 @@ class Seq
     strand  = '+'
 
     while (sum / self.seq.length) < max_cov
-      if self.seq.size - size == 0
-        start = 0
-      else
-        start = rand(self.seq.size - size)
-      end
-
-      stop     = start + size - 1
-      seq_name = self.seq_name + "[#{start + 1}-#{stop + 1}:#{strand}]"
-      seq      = self.seq[start .. stop]
-      entry    = Seq.new(seq_name, seq, 'dna')
-
-      entry.revcomp if strand == '-'
+      entry = get_random_seq(size, strand)
 
       if block_given?
         yield entry
@@ -76,6 +65,29 @@ class Seq
 
     entries
   end
+
+  private
+
+  # Method that picks a random subsequence of a given size from a sequence.
+  # The position of the subsequence is appended to the sequence name along
+  # with the strand. The sequence is reverse complemented in case of minus
+  # strand.
+  def get_random_seq(size, strand)
+    if self.seq.size - size == 0
+      start = 0
+    else
+      start = rand(self.seq.size - size)
+    end
+
+    stop     = start + size - 1
+    seq_name = self.seq_name + "[#{start + 1}-#{stop + 1}:#{strand}]"
+    seq      = self.seq[start .. stop]
+    entry    = Seq.new(seq_name, seq, 'dna')
+
+    entry.revcomp if strand == '-'
+
+    entry
+  end
 end
 
 casts = []