cleaning up digest.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1638 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/digest_seq b/bp_bin/digest_seq
index 56fa32253692642641c88f80d50216851c7364cd..fa6cf8ef412df1b28199e050c94f612ac32a8cda 100755 (executable)
--- 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 1c6f245b3672d0705fee06cc9e9ac6e043db4b11..b2b7fd76e301977ae0b78e2c2939fb7c88296c70 100644 (file)
--- 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 1e09f9697cdd6cc7c66d0e877e1f2f15e6aa514f..0916c1f466a1fb3479914bae4f163f1704a7b4a7 100755 (executable)
--- 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'