genfrag 0.0.0.3 → 0.0.0.4

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Binary file
@@ -2,7 +2,7 @@
2
2
  module Genfrag
3
3
 
4
4
  # :stopdoc:
5
- VERSION = '0.0.0.3'
5
+ VERSION = '0.0.0.4'
6
6
  LIBPATH = ::File.expand_path(::File.dirname(__FILE__)) + ::File::SEPARATOR
7
7
  PATH = ::File.dirname(LIBPATH) + ::File::SEPARATOR
8
8
  # :startdoc:
@@ -132,14 +132,16 @@ class SearchCommand < Command
132
132
  @sequences = processed_fasta_file
133
133
  @adapters = {}
134
134
  @re5_ds, @re3_ds = [@ops.re5, @ops.re3].map {|x| Bio::RestrictionEnzyme::DoubleStranded.new(x)}
135
+ @re5_ds_aligned_strands_with_cuts_primary = @re5_ds.aligned_strands_with_cuts.primary
136
+ @re3_ds_aligned_strands_with_cuts_primary = @re3_ds.aligned_strands_with_cuts.primary
135
137
  if @ops.verbose
136
138
  cli_p(cli, <<-END
137
139
  RE5: #{@ops.re5}
138
- #{@re5_ds.aligned_strands_with_cuts.primary}
140
+ #{@re5_ds_aligned_strands_with_cuts_primary}
139
141
  #{@re5_ds.aligned_strands_with_cuts.complement}
140
142
 
141
143
  RE3: #{@ops.re3}
142
- #{@re3_ds.aligned_strands_with_cuts.primary}
144
+ #{@re5_ds_aligned_strands_with_cuts_primary}
143
145
  #{@re3_ds.aligned_strands_with_cuts.complement}
144
146
 
145
147
  adapter5: #{@ops.adapter5}
@@ -224,12 +226,12 @@ END
224
226
 
225
227
  # note the next two if-statements at this level chain together with 'p' and 'c'
226
228
  if @adapters[:adapter5_specificity]
227
- p, c = matches_adapter(5, p, c, raw_frag, @trim)
229
+ p, c = matches_adapter(5, p, c, raw_frag, @trim, @re5_ds_aligned_strands_with_cuts_primary)
228
230
  next if !p # next if returned false -- no match
229
231
  end
230
232
 
231
233
  if @adapters[:adapter3_specificity]
232
- p, c = matches_adapter(3, p, c, raw_frag, @trim)
234
+ p, c = matches_adapter(3, p, c, raw_frag, @trim, @re3_ds_aligned_strands_with_cuts_primary)
233
235
  next if !p # next if returned false -- no match
234
236
  end
235
237
 
@@ -6,7 +6,7 @@ class SearchCommand < Command
6
6
 
7
7
  # Does the sequence match the adapter
8
8
  #
9
- def matches_adapter(five_or_three, primary_frag, complement_frag, raw_frag, trim)
9
+ def matches_adapter(five_or_three, primary_frag, complement_frag, raw_frag, trim, primary_strand)
10
10
  adapter_specificity = nil
11
11
  adapter_sequence = nil
12
12
  adapter_size = nil
@@ -14,7 +14,7 @@ class SearchCommand < Command
14
14
  trim_complement = nil
15
15
 
16
16
  if five_or_three == 5
17
- tail = right_tail_of(Bio::RestrictionEnzyme::DoubleStranded.new(@ops.re5).aligned_strands_with_cuts.primary)
17
+ tail = right_tail_of(primary_strand)
18
18
 
19
19
  adapter_specificity = @adapters[:adapter5_specificity].upcase
20
20
  adapter_sequence = @adapters[:adapter5_sequence].upcase if @adapters[:adapter5_sequence]
@@ -30,7 +30,7 @@ class SearchCommand < Command
30
30
  return false if primary_frag[ lead_in .. -1 ].tr('.', '') !~ /^#{adapter_specificity}/i
31
31
 
32
32
  elsif five_or_three == 3
33
- tail = left_tail_of(Bio::RestrictionEnzyme::DoubleStranded.new(@ops.re3).aligned_strands_with_cuts.primary)
33
+ tail = left_tail_of(primary_strand)
34
34
 
35
35
  if @adapters[:adapter3_specificity][0].chr == '_'
36
36
  adapter_specificity = @adapters[:adapter3_specificity][1..-1].reverse.upcase
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: genfrag
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.0.0.3
4
+ version: 0.0.0.4
5
5
  platform: ruby
6
6
  authors:
7
7
  - Pjotr Prins and Trevor Wennblom
@@ -9,7 +9,7 @@ autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
11
 
12
- date: 2009-08-06 00:00:00 -05:00
12
+ date: 2009-08-20 00:00:00 -05:00
13
13
  default_executable:
14
14
  dependencies:
15
15
  - !ruby/object:Gem::Dependency
@@ -30,7 +30,7 @@ dependencies:
30
30
  requirements:
31
31
  - - ">="
32
32
  - !ruby/object:Gem::Version
33
- version: 0.8.4
33
+ version: 0.8.7
34
34
  version:
35
35
  - !ruby/object:Gem::Dependency
36
36
  name: bones
@@ -54,6 +54,7 @@ extra_rdoc_files:
54
54
  - README.rdoc
55
55
  - bin/genfrag
56
56
  files:
57
+ - .DS_Store
57
58
  - .bnsignore
58
59
  - History.txt
59
60
  - LICENSE.txt