From 525d168fa9084e4ebdd42b3fc05b91c974cf9d38 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Sun, 13 Nov 2011 18:58:16 +0000
Subject: [PATCH] cleaning up digest.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1638 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/digest_seq                    |  6 ++----
 code_ruby/lib/maasha/seq.rb          |  1 -
 code_ruby/test/maasha/test_digest.rb | 26 ++++++++++++++++++++++++++
 3 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 56fa322..fa6cf8e 100755
--- a/bp_bin/digest_seq
+++ b/bp_bin/digest_seq
@@ -28,7 +28,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
 require 'maasha/biopieces'
 require 'maasha/seq'
 
@@ -41,11 +40,11 @@ options = Biopieces.options_parse(ARGV, casts)
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record.has_key? :SEQ_NAME and record.has_key? :SEQ
-      seq    = Seq.new(record[:SEQ_NAME], record[:SEQ])
+      seq    = Seq.new_bp(record)
       digest = Digest.new(seq, options[:pattern].to_s, options[:cut_pos])
 
       digest.each do |subseq|
-        new_record            = subseq.to_bp
+        new_record = subseq.to_bp
 
         if new_record[:SEQ_NAME] =~ /\[(\d+)-(\d+)\]$/
           s_beg = $1
@@ -63,7 +62,6 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   end
 end
 
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
diff --git a/code_ruby/lib/maasha/seq.rb b/code_ruby/lib/maasha/seq.rb
index 1c6f245..b2b7fd7 100644
--- a/code_ruby/lib/maasha/seq.rb
+++ b/code_ruby/lib/maasha/seq.rb
@@ -22,7 +22,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-require 'maasha/digest'
 require 'maasha/patternmatcher'
 require 'maasha/bits'
 #require 'maasha/patscan'
diff --git a/code_ruby/test/maasha/test_digest.rb b/code_ruby/test/maasha/test_digest.rb
index 1e09f96..0916c1f 100755
--- a/code_ruby/test/maasha/test_digest.rb
+++ b/code_ruby/test/maasha/test_digest.rb
@@ -1,6 +1,32 @@
 #!/usr/bin/env ruby
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# This software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/seq'
+require 'maasha/digest'
 require 'test/unit'
 require 'pp'
 
-- 
2.39.2