genfrag 0.0.0.3 → 0.0.0.4

data/lib/genfrag.rb

@@ -2,7 +2,7 @@
 module Genfrag
 
   # :stopdoc:
-  VERSION = '0.0.0.3'
+  VERSION = '0.0.0.4'
   LIBPATH = ::File.expand_path(::File.dirname(__FILE__)) + ::File::SEPARATOR
   PATH = ::File.dirname(LIBPATH) + ::File::SEPARATOR
   # :startdoc:

data/lib/genfrag/app/search_command.rb

@@ -132,14 +132,16 @@ class SearchCommand < Command
     @sequences = processed_fasta_file
     @adapters = {}
     @re5_ds, @re3_ds = [@ops.re5, @ops.re3].map {|x| Bio::RestrictionEnzyme::DoubleStranded.new(x)}
+    @re5_ds_aligned_strands_with_cuts_primary = @re5_ds.aligned_strands_with_cuts.primary
+    @re3_ds_aligned_strands_with_cuts_primary = @re3_ds.aligned_strands_with_cuts.primary
     if @ops.verbose
       cli_p(cli, <<-END
 RE5: #{@ops.re5}
-#{@re5_ds.aligned_strands_with_cuts.primary}
+#{@re5_ds_aligned_strands_with_cuts_primary}
 #{@re5_ds.aligned_strands_with_cuts.complement}
 
 RE3: #{@ops.re3}
-#{@re3_ds.aligned_strands_with_cuts.primary}
+#{@re5_ds_aligned_strands_with_cuts_primary}
 #{@re3_ds.aligned_strands_with_cuts.complement}
 
 adapter5: #{@ops.adapter5}
@@ -224,12 +226,12 @@ END
         
       # note the next two if-statements at this level chain together with 'p' and 'c'
         if @adapters[:adapter5_specificity]
-          p, c = matches_adapter(5, p, c, raw_frag, @trim)
+          p, c = matches_adapter(5, p, c, raw_frag, @trim, @re5_ds_aligned_strands_with_cuts_primary)
           next if !p  # next if returned false -- no match
         end
         
         if @adapters[:adapter3_specificity]
-          p, c = matches_adapter(3, p, c, raw_frag, @trim)
+          p, c = matches_adapter(3, p, c, raw_frag, @trim, @re3_ds_aligned_strands_with_cuts_primary)
           next if !p  # next if returned false -- no match
         end
         

data/lib/genfrag/app/search_command/match.rb

@@ -6,7 +6,7 @@ class SearchCommand < Command
 
 # Does the sequence match the adapter
 #
-  def matches_adapter(five_or_three, primary_frag, complement_frag, raw_frag, trim)
+  def matches_adapter(five_or_three, primary_frag, complement_frag, raw_frag, trim, primary_strand)
     adapter_specificity = nil
     adapter_sequence    = nil
     adapter_size        = nil
@@ -14,7 +14,7 @@ class SearchCommand < Command
     trim_complement     = nil
 
     if five_or_three == 5
-      tail = right_tail_of(Bio::RestrictionEnzyme::DoubleStranded.new(@ops.re5).aligned_strands_with_cuts.primary)
+      tail = right_tail_of(primary_strand)
 
       adapter_specificity = @adapters[:adapter5_specificity].upcase
       adapter_sequence    = @adapters[:adapter5_sequence].upcase if @adapters[:adapter5_sequence]
@@ -30,7 +30,7 @@ class SearchCommand < Command
       return false if primary_frag[ lead_in .. -1 ].tr('.', '') !~ /^#{adapter_specificity}/i
 
     elsif five_or_three == 3
-      tail = left_tail_of(Bio::RestrictionEnzyme::DoubleStranded.new(@ops.re3).aligned_strands_with_cuts.primary)
+      tail = left_tail_of(primary_strand)
 
       if @adapters[:adapter3_specificity][0].chr == '_'
         adapter_specificity = @adapters[:adapter3_specificity][1..-1].reverse.upcase

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: genfrag
 version: !ruby/object:Gem::Version 
-  version: 0.0.0.3
+  version: 0.0.0.4
 platform: ruby
 authors: 
 - Pjotr Prins and Trevor Wennblom
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2009-08-06 00:00:00 -05:00
+date: 2009-08-20 00:00:00 -05:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -30,7 +30,7 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        version: 0.8.4
+        version: 0.8.7
     version: 
 - !ruby/object:Gem::Dependency 
   name: bones
@@ -54,6 +54,7 @@ extra_rdoc_files:
 - README.rdoc
 - bin/genfrag
 files: 
+- .DS_Store
 - .bnsignore
 - History.txt
 - LICENSE.txt