bio-bigbio 0.1.5 → 0.1.6

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@@ -0,0 +1,7 @@
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+ ---
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+ SHA1:
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+ metadata.gz: 358cea2b69da2db20774ab98b4c0dfaa561b32c6
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+ data.tar.gz: 1e1baca80f0aa0fd26d579e158aa88e0361493e9
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+ SHA512:
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+ metadata.gz: ac532f773fd025ee927bfff89a96d142b2d9b9ca28f14a2bd368553a164026bd2530d4f4f95e2addcc30ae323d6b58ed5c30111335927c2e66630933ee16f75c
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+ data.tar.gz: b228c3d346a4cf87f9fec71392336d9e66be1c721f8dae167553ecac5a92b689cd9420a0206ef31fee4dd4e9df43ea5a97472474a07cb4ed1da0bd553a013473
data/Gemfile CHANGED
@@ -1,15 +1,11 @@
1
1
  source "http://rubygems.org"
2
- # Add dependencies required to use your gem here.
3
- # Example:
4
- # gem "activesupport", ">= 2.3.5"
5
2
  gem "bio", ">= 1.4.1"
6
- gem "bio-logger", ">= 0.9.0"
3
+ gem "bio-logger"
7
4
 
8
5
  # Add dependencies to develop your gem here.
9
6
  # Include everything needed to run rake, tests, features, etc.
10
7
  group :development do
11
- gem "rspec", "~> 2.3.0"
12
- gem "bundler", "~> 1.0.0"
13
- gem "jeweler", "~> 1.5.2"
14
- gem "rcov", ">= 0"
8
+ gem "rspec"
9
+ gem "bundler"
10
+ gem "jeweler"
15
11
  end
@@ -1,34 +1,72 @@
1
1
  GEM
2
2
  remote: http://rubygems.org/
3
3
  specs:
4
- bio (1.4.1)
5
- bio-logger (0.9.0)
4
+ addressable (2.3.6)
5
+ bio (1.4.3)
6
+ bio-logger (1.0.1)
6
7
  log4r (>= 1.1.9)
7
- diff-lcs (1.1.2)
8
- git (1.2.5)
9
- jeweler (1.5.2)
10
- bundler (~> 1.0.0)
8
+ builder (3.2.2)
9
+ descendants_tracker (0.0.4)
10
+ thread_safe (~> 0.3, >= 0.3.1)
11
+ diff-lcs (1.1.3)
12
+ faraday (0.9.0)
13
+ multipart-post (>= 1.2, < 3)
14
+ git (1.2.6)
15
+ github_api (0.11.3)
16
+ addressable (~> 2.3)
17
+ descendants_tracker (~> 0.0.1)
18
+ faraday (~> 0.8, < 0.10)
19
+ hashie (>= 1.2)
20
+ multi_json (>= 1.7.5, < 2.0)
21
+ nokogiri (~> 1.6.0)
22
+ oauth2
23
+ hashie (2.1.1)
24
+ highline (1.6.21)
25
+ jeweler (2.0.1)
26
+ builder
27
+ bundler (>= 1.0)
11
28
  git (>= 1.2.5)
29
+ github_api
30
+ highline (>= 1.6.15)
31
+ nokogiri (>= 1.5.10)
12
32
  rake
13
- log4r (1.1.9)
14
- rake (0.8.7)
15
- rcov (0.9.9)
16
- rspec (2.3.0)
17
- rspec-core (~> 2.3.0)
18
- rspec-expectations (~> 2.3.0)
19
- rspec-mocks (~> 2.3.0)
20
- rspec-core (2.3.1)
21
- rspec-expectations (2.3.0)
22
- diff-lcs (~> 1.1.2)
23
- rspec-mocks (2.3.0)
33
+ rdoc
34
+ json (1.8.1)
35
+ jwt (0.1.11)
36
+ multi_json (>= 1.5)
37
+ log4r (1.1.10)
38
+ mini_portile (0.5.3)
39
+ multi_json (1.9.3)
40
+ multi_xml (0.5.5)
41
+ multipart-post (2.0.0)
42
+ nokogiri (1.6.1)
43
+ mini_portile (~> 0.5.0)
44
+ oauth2 (0.9.3)
45
+ faraday (>= 0.8, < 0.10)
46
+ jwt (~> 0.1.8)
47
+ multi_json (~> 1.3)
48
+ multi_xml (~> 0.5)
49
+ rack (~> 1.2)
50
+ rack (1.5.2)
51
+ rake (10.3.1)
52
+ rdoc (4.1.1)
53
+ json (~> 1.4)
54
+ rspec (2.10.0)
55
+ rspec-core (~> 2.10.0)
56
+ rspec-expectations (~> 2.10.0)
57
+ rspec-mocks (~> 2.10.0)
58
+ rspec-core (2.10.1)
59
+ rspec-expectations (2.10.0)
60
+ diff-lcs (~> 1.1.3)
61
+ rspec-mocks (2.10.1)
62
+ thread_safe (0.3.3)
24
63
 
25
64
  PLATFORMS
26
65
  ruby
27
66
 
28
67
  DEPENDENCIES
29
68
  bio (>= 1.4.1)
30
- bio-logger (>= 0.9.0)
31
- bundler (~> 1.0.0)
32
- jeweler (~> 1.5.2)
33
- rcov
34
- rspec (~> 2.3.0)
69
+ bio-logger
70
+ bundler
71
+ jeweler
72
+ rspec
@@ -1,4 +1,4 @@
1
- Copyright (c) 2011-2013 Pjotr Prins
1
+ Copyright (c) 2011-2014 Pjotr Prins
2
2
 
3
3
  Permission is hereby granted, free of charge, to any person obtaining
4
4
  a copy of this software and associated documentation files (the
data/README.md CHANGED
@@ -79,6 +79,12 @@ so to skip every other record
79
79
  fasta_filter.rb --filter "num % 2 == 0"
80
80
  ```
81
81
 
82
+ Find all sequences that contain a stop codon in the sequence
83
+
84
+ ```sh
85
+ fasta_filter.rb --filter 'rec.seq =~ /\*./' aa.fa
86
+ ```
87
+
82
88
  Rewrite all sequences to lower case, you can use the useful rewrite
83
89
  option
84
90
 
@@ -86,7 +92,20 @@ option
86
92
  fasta_filter.rb --rewrite 'rec.seq = rec.seq.downcase'
87
93
  ```
88
94
 
89
- Filters and rewrites can be combined. The rest is up to your imagination!
95
+ Rewrite the FASTA descriptors
96
+
97
+ ```sh
98
+ fasta_filter.rb --rewrite 'rec.descr =~ /gene=(\S+)/; rec.descr = $1' test.fa
99
+ ```
100
+
101
+ Filters and rewrites can be combined. The rest is up to your
102
+ imagination! One final example to remove low quality sequences from an
103
+ amino acid file (one amino acid dominates):
104
+
105
+ ```sh
106
+ fasta_filter.rb --filter "count = {} ; rec.seq.each_char { |c| count[c] ||= 1 ; count[c] += 1 }; count.values.max.to_f/rec.seq.size < 0.30" < aa.fa > aa1.fa
107
+ ```
108
+
90
109
 
91
110
  # API Examples
92
111
 
@@ -227,9 +246,9 @@ If you use this software, please cite one of
227
246
 
228
247
  # Biogems.info
229
248
 
230
- This Biogem is published at [#bio-table](http://biogems.info/index.html)
249
+ This Biogem is published on [biogems.info](http://biogems.info/index.html#bigbio)
231
250
 
232
251
  # Copyright
233
252
 
234
- Copyright (c) 2011-2013 Pjotr Prins. See LICENSE for further details.
253
+ Copyright (c) 2011-2014 Pjotr Prins. See LICENSE for further details.
235
254
 
data/Rakefile CHANGED
@@ -40,7 +40,7 @@ end
40
40
  task :test => :spec
41
41
  task :default => :spec
42
42
 
43
- require 'rake/rdoctask'
43
+ require 'rdoc/task'
44
44
  Rake::RDocTask.new do |rdoc|
45
45
  version = File.exist?('VERSION') ? File.read('VERSION') : ""
46
46
 
data/VERSION CHANGED
@@ -1 +1 @@
1
- 0.1.5
1
+ 0.1.6
@@ -60,6 +60,8 @@ class OptParser
60
60
  opts.separator " fasta_filter.rb --filter \"rec.descr =~ /C. elegans/\" test/data/fasta/nt.fa"
61
61
  opts.separator " fasta_filter.rb --filter \"num % 2 == 0\" test/data/fasta/nt.fa"
62
62
  opts.separator " fasta_filter.rb test/data/fasta/nt.fa --rewrite 'rec.seq.downcase!'"
63
+ opts.separator " fasta_filter.rb --rewrite 'rec.descr =~ /gene=(\S+)/; rec.descr = $1' test.fa"
64
+ opts.separator " fasta_filter.rb --filter 'rec.seq =~ /\*./' aa.fa"
63
65
  opts.separator ""
64
66
  opts.separator "Other options:"
65
67
  opts.separator ""
data/bin/getorf CHANGED
@@ -1,4 +1,4 @@
1
- #! /usr/bin/ruby
1
+ #! /usr/bin/env ruby
2
2
  #
3
3
  # Predict ORF's from nucleotide sequences using the BigBio predictors.
4
4
  # The input is a fasta file, the output consists of
@@ -1,4 +1,4 @@
1
- #! /usr/bin/ruby
1
+ #! /usr/bin/env ruby
2
2
  #
3
3
  # Translate nucleotide sequences into aminoacids sequences in all
4
4
  # reading frames.
@@ -5,11 +5,11 @@
5
5
 
6
6
  Gem::Specification.new do |s|
7
7
  s.name = "bio-bigbio"
8
- s.version = "0.1.5"
8
+ s.version = "0.1.6"
9
9
 
10
10
  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
11
11
  s.authors = ["Pjotr Prins"]
12
- s.date = "2013-05-03"
12
+ s.date = "2014-05-16"
13
13
  s.description = "Fasta reader, ORF emitter, sequence translation"
14
14
  s.email = "pjotr.public01@thebird.nl"
15
15
  s.executables = ["fasta_filter.rb", "fasta_sort.rb", "getorf", "nt2aa.rb"]
@@ -63,44 +63,31 @@ Gem::Specification.new do |s|
63
63
  s.homepage = "http://github.com/pjotrp/bigbio"
64
64
  s.licenses = ["MIT"]
65
65
  s.require_paths = ["lib"]
66
- s.rubygems_version = "1.8.10"
66
+ s.rubygems_version = "1.8.23"
67
67
  s.summary = "Low memory sequence emitters"
68
- s.test_files = [
69
- "spec/emitter_spec.rb",
70
- "spec/predictorf_spec.rb",
71
- "test/doctest/test_fasta.rb",
72
- "test/doctest/test_frames.rb",
73
- "test/doctest/test_getorf.rb",
74
- "test/doctest/test_paired.rb",
75
- "test/performance/translate_with_biolib.rb",
76
- "test/performance/translate_with_bioruby.rb"
77
- ]
78
68
 
79
69
  if s.respond_to? :specification_version then
80
70
  s.specification_version = 3
81
71
 
82
72
  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
83
73
  s.add_runtime_dependency(%q<bio>, [">= 1.4.1"])
84
- s.add_runtime_dependency(%q<bio-logger>, [">= 0.9.0"])
85
- s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
86
- s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
87
- s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
88
- s.add_development_dependency(%q<rcov>, [">= 0"])
74
+ s.add_runtime_dependency(%q<bio-logger>, [">= 0"])
75
+ s.add_development_dependency(%q<rspec>, [">= 0"])
76
+ s.add_development_dependency(%q<bundler>, [">= 0"])
77
+ s.add_development_dependency(%q<jeweler>, [">= 0"])
89
78
  else
90
79
  s.add_dependency(%q<bio>, [">= 1.4.1"])
91
- s.add_dependency(%q<bio-logger>, [">= 0.9.0"])
92
- s.add_dependency(%q<rspec>, ["~> 2.3.0"])
93
- s.add_dependency(%q<bundler>, ["~> 1.0.0"])
94
- s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
95
- s.add_dependency(%q<rcov>, [">= 0"])
80
+ s.add_dependency(%q<bio-logger>, [">= 0"])
81
+ s.add_dependency(%q<rspec>, [">= 0"])
82
+ s.add_dependency(%q<bundler>, [">= 0"])
83
+ s.add_dependency(%q<jeweler>, [">= 0"])
96
84
  end
97
85
  else
98
86
  s.add_dependency(%q<bio>, [">= 1.4.1"])
99
- s.add_dependency(%q<bio-logger>, [">= 0.9.0"])
100
- s.add_dependency(%q<rspec>, ["~> 2.3.0"])
101
- s.add_dependency(%q<bundler>, ["~> 1.0.0"])
102
- s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
103
- s.add_dependency(%q<rcov>, [">= 0"])
87
+ s.add_dependency(%q<bio-logger>, [">= 0"])
88
+ s.add_dependency(%q<rspec>, [">= 0"])
89
+ s.add_dependency(%q<bundler>, [">= 0"])
90
+ s.add_dependency(%q<jeweler>, [">= 0"])
104
91
  end
105
92
  end
106
93
 
@@ -22,7 +22,7 @@ begin
22
22
  Bio::Big::Environment.instance.biolib = true
23
23
  rescue LoadError
24
24
  log.outputters = Bio::Log::Outputter.stderr
25
- log.warn "BioLib functionality not loaded"
25
+ log.debug "BioLib functionality not loaded"
26
26
  end
27
27
 
28
28
  require 'bio'
@@ -10,7 +10,7 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
10
10
 
11
11
  it "should emit small parts" do
12
12
  s = ""
13
- FastaEmitter.new("test/data/fasta/nt.fa",10).emit_seq do | part, index, tag, seq |
13
+ Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa",10).emit_seq do | part, index, tag, seq |
14
14
  # p [index, part, tag, seq]
15
15
  s += seq
16
16
  if index == 95 and part == :tail
@@ -38,7 +38,7 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
38
38
  end
39
39
 
40
40
  it "should emit large parts" do
41
- FastaEmitter.new("test/data/fasta/nt.fa").emit_seq do | part, index, tag, seq |
41
+ Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa").emit_seq do | part, index, tag, seq |
42
42
  # p [index, part, tag, seq]
43
43
  if index == 95
44
44
  seq.should == "ATCATTAGCAACACCAGCTTCCTCTCTCTCGCTTCAAAGTTCACTACTCGTGGATCTCGTCTTCAGTGTACAGTATCAAGGGCTCGATCTGCGGTGGATGAGACATCAGATTCAGGAGCTTTTCAAAGAACTGCATCGACATCCGTAACTTCGTTTCAAAAGATTCCAATTCTCAGTTTCAGCTGAATCTGGTAGATACCATCTTTACATATCGTATGCTTGTCATGGGCTTCTAGATGCCTTTCATACTTAAAGATCAAAGGACTTGACGATGCAATAAGCTTCTCGTCTGTAAAACCC"
@@ -47,12 +47,12 @@ describe Bio::Big::FastaEmitter, "when using the emitter" do
47
47
  end
48
48
  end
49
49
 
50
- describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
50
+ describe Bio::Big::ShortFrameState, "when using the Bio::Big::ShortFrameState" do
51
51
 
52
52
  include Bio::Big
53
53
 
54
54
  it "should find an ORF" do
55
- fr = ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,0
55
+ fr = Bio::Big::ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,0
56
56
  orfs = fr.get_stopstop_orfs
57
57
  orfs.map{ | orf | orf.pos }.should == [ 3, 5 ]
58
58
  orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA", "TGGATTTAA"]
@@ -61,14 +61,14 @@ describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
61
61
  orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTAA","ATGTAA"]
62
62
  end
63
63
  it "should handle min_size" do
64
- fr = ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,9
64
+ fr = Bio::Big::ShortFrameState.new "atggattaaatgtaatggatttaatgtaaa",0,9
65
65
  orfs = fr.get_stopstop_orfs
66
66
  orfs.map{ | orf | orf.to_seq }.should == [ "TGGATTTAA"]
67
67
  orfs.map{ | orf | orf.pos }.should == [ 5 ]
68
68
  fr.get_startstop_orfs.should == []
69
69
  end
70
70
  it "should find ORFs in" do
71
- fr = ShortFrameState.new "atgttttaaatgtaatgttgttaaatgttttaaatgtaatgttgttaa",0,0
71
+ fr = Bio::Big::ShortFrameState.new "atgttttaaatgtaatgttgttaaatgttttaaatgtaatgttgttaa",0,0
72
72
  orfs = fr.get_stopstop_orfs
73
73
  orfs.map{ | orf | orf.to_seq }.should == ["ATGTAA", "TGTTGTTAA", "ATGTTTTAA", "ATGTAA", "TGTTGTTAA"]
74
74
  orfs.map{ | orf | orf.pos }.should == [3, 5, 8, 11, 13]
@@ -108,17 +108,17 @@ describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
108
108
 
109
109
  # Frame 0
110
110
  minsize = 0
111
- fr = ShortFrameState.new s,0,minsize
111
+ fr = Bio::Big::ShortFrameState.new s,0,minsize
112
112
  orfs = fr.get_stopstop_orfs
113
113
  orfs.map{ | orf | orf.to_seq }.should == []
114
114
 
115
115
  # Frame 1
116
- fr = ShortFrameState.new s[1..-1],0,minsize
116
+ fr = Bio::Big::ShortFrameState.new s[1..-1],0,minsize
117
117
  os = fr.get_stopstop_orfs
118
118
  os.map{ | orf | orf.to_seq }.should == ["TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"]
119
119
  orfs += os
120
120
  # Frame 2
121
- fr = ShortFrameState.new s[2..-1],0,minsize
121
+ fr = Bio::Big::ShortFrameState.new s[2..-1],0,minsize
122
122
  os = fr.get_stopstop_orfs
123
123
  os.map{ | orf | orf.to_seq }.should == ["GCGGANCGGTAA", "GAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAA", "GGTCCTTGTCACAGATGA", "GGCTCGTAG"]
124
124
  orfs += os
@@ -132,14 +132,14 @@ describe Bio::Big::ShortFrameState, "when using the ShortFrameState" do
132
132
 
133
133
  # Frame 0
134
134
  minsize = 0
135
- fr = ShortFrameState.new s,0,minsize
135
+ fr = Bio::Big::ShortFrameState.new s,0,minsize
136
136
  orfs = fr.get_startstop_orfs
137
137
 
138
138
  # Frame 1
139
- fr = ShortFrameState.new s[1..-1],0,minsize
139
+ fr = Bio::Big::ShortFrameState.new s[1..-1],0,minsize
140
140
  orfs += fr.get_startstop_orfs
141
141
  # Frame 2
142
- fr = ShortFrameState.new s[2..-1],0,minsize
142
+ fr = Bio::Big::ShortFrameState.new s[2..-1],0,minsize
143
143
  orfs += fr.get_startstop_orfs
144
144
  orfs.map{ | orf | orf.to_seq }.should == []
145
145
  orfs.size.should == 0
@@ -151,11 +151,11 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
151
151
  it "should combine a forward frame" do
152
152
  s1 = "atggattaaatgtaata"
153
153
  s2 = "atggatttaatgtaaa"
154
- fr = ShortFrameState.new s1,0,0
154
+ fr = Bio::Big::ShortFrameState.new s1,0,0
155
155
  fr.ntseq_pos.should == 0
156
156
  orfs = fr.get_stopstop_orfs
157
157
  orfs.size == 1 # in codons
158
- fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
158
+ fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
159
159
  fr3.ntseq_pos.should == 15
160
160
  fr3.codons.to_seq.should == "TAATGGATTTAATGTAAA"
161
161
  norfs = fr3.get_stopstop_orfs
@@ -169,11 +169,11 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
169
169
  # ......---===xx
170
170
  s2 = "atggatttaattattataaa"
171
171
  # x======xxx======xxx.
172
- fr = ShortFrameState.new s1,0,0
172
+ fr = Bio::Big::ShortFrameState.new s1,0,0
173
173
  fr.ntseq_pos.should == 0
174
174
  orfs = fr.get_stopstop_orfs
175
175
  orfs.size == 0 # in codons
176
- fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
176
+ fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
177
177
  fr3.ntseq_pos.should == 0
178
178
  fr3.codons.to_seq.should == "ATGGATTAAATGTAATGGATTTAATTATTATAA"
179
179
  norfs = fr3.get_stopstop_orfs
@@ -187,11 +187,11 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
187
187
  # ......---===xx
188
188
  s2 = "atggatttaatgtaaa"
189
189
  # x======xxx
190
- fr = ShortFrameState.new s1,0,0
190
+ fr = Bio::Big::ShortFrameState.new s1,0,0
191
191
  fr.ntseq_pos.should == 0
192
192
  orfs = fr.get_stopstop_orfs
193
193
  orfs.size == 0 # in codons
194
- fr3 = FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
194
+ fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_right(fr,orfs,s2)
195
195
  # p fr3
196
196
  fr3.ntseq_pos.should == 0 # on the combined sequences
197
197
  fr3.codons.to_seq.should == "ATGGATTAAATGTAATGGATTTAATGTAAA"
@@ -221,14 +221,14 @@ describe Bio::Big::ShortFrameState, "when combining frames" do
221
221
  s1 = "atggattaaatgta"
222
222
  # ......xxx=====
223
223
  # now move the other way, as sequences get emitted on the left
224
- fr = ShortReversedFrameState.new s2,0,0
224
+ fr = Bio::Big::ShortReversedFrameState.new s2,0,0
225
225
  # p fr
226
226
  fr.codons.to_seq.should == "ATTTAAATGGATTTAATGTAAATT"
227
227
  fr.ntseq_pos.should == 0
228
228
  orfs = fr.get_stopstop_orfs
229
229
  orfs.map{ | orf | orf.to_seq }.should == ["ATGGATTTAATGTAA"]
230
230
  orfs.first.pos.should == 2 # in codons
231
- fr3 = FrameCodonHelpers::CreateShortFrame.create_left(fr,orfs,s1)
231
+ fr3 = Bio::Big::FrameCodonHelpers::CreateShortFrame.create_left(fr,orfs,s1)
232
232
  fr3.ntseq_pos.should == 18 # 6 codons
233
233
  fr3.codons.to_seq.should == "ATGGATTAAATGTATATTTAA"
234
234
  norfs = fr3.get_stopstop_orfs
@@ -244,9 +244,9 @@ describe Bio::Big::OrfEmitter, "when using the ORF emitter" do
244
244
  include Bio::Big
245
245
 
246
246
  it "should emit STOP-STOP ORFs in all frames" do
247
- f = FastaEmitter.new("test/data/fasta/nt.fa")
247
+ f = Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa")
248
248
  seqs = []
249
- OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
249
+ Bio::Big::OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
250
250
  break if index != 0
251
251
  if frame == 0 and index == 0 and pos == 39
252
252
  seq.should == "TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"
@@ -259,9 +259,9 @@ describe Bio::Big::OrfEmitter, "when using the ORF emitter" do
259
259
  seqs.join(';')[50..350].should == "TNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA;GCAAAGAGCGAGAAAATGAGCGGANCGGTAAGAAAATCGCGGATGTGGCTTTCAAAGCTTCAAGGACTATCGATTGGGATGGTATGGCTAAGGTCCTTGTCACAGATGAGGCTCGTAGAGAGTTCTCTAACCTTCGTCGTGCTTTCGATGAGGTTAACACACAGCTCCAGACCAAATTTAGTCAGGACCT"
260
260
  end
261
261
  it "should emit STOP-STOP ORFs in all frames using a shorter emitter" do
262
- f = FastaEmitter.new("test/data/fasta/nt.fa",150)
262
+ f = Bio::Big::FastaEmitter.new("test/data/fasta/nt.fa",150)
263
263
  seqs = []
264
- OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
264
+ Bio::Big::OrfEmitter.new(f,:stopstop)::emit_seq do | frame, index, tag, pos, seq |
265
265
  break if index != 0
266
266
  if frame == 0 and index == 0 and pos == 39
267
267
  seq.should == "TTNCGCGTGCCGCCTTCTTTCTCCTTTTTCTCTTTTACTTCTTCATCATCATCTTCTTCTTCTTCCTCTTCGATATTCGTCAGTGTGTGTATTTTGGGGAAAACTTTGTGA"
@@ -1,4 +1,4 @@
1
- #! /usr/bin/ruby
1
+ #! /usr/bin/env ruby
2
2
  #
3
3
  # Performance testing routing for translating a FASTA file into six
4
4
  # reading frames using the Biolib (EMBOSS) routines.
@@ -1,4 +1,4 @@
1
- #! /usr/bin/ruby
1
+ #! /usr/bin/env ruby
2
2
  #
3
3
  # Performance testing routing for translating a FASTA file into six
4
4
  # reading frames using the Bioruby routines.
metadata CHANGED
@@ -1,82 +1,85 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bio-bigbio
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.1.5
5
- prerelease:
4
+ version: 0.1.6
6
5
  platform: ruby
7
6
  authors:
8
7
  - Pjotr Prins
9
8
  autorequire:
10
9
  bindir: bin
11
10
  cert_chain: []
12
- date: 2013-05-03 00:00:00.000000000Z
11
+ date: 2014-05-16 00:00:00.000000000 Z
13
12
  dependencies:
14
13
  - !ruby/object:Gem::Dependency
15
14
  name: bio
16
- requirement: &27203900 !ruby/object:Gem::Requirement
17
- none: false
15
+ requirement: !ruby/object:Gem::Requirement
18
16
  requirements:
19
- - - ! '>='
17
+ - - ">="
20
18
  - !ruby/object:Gem::Version
21
19
  version: 1.4.1
22
20
  type: :runtime
23
21
  prerelease: false
24
- version_requirements: *27203900
22
+ version_requirements: !ruby/object:Gem::Requirement
23
+ requirements:
24
+ - - ">="
25
+ - !ruby/object:Gem::Version
26
+ version: 1.4.1
25
27
  - !ruby/object:Gem::Dependency
26
28
  name: bio-logger
27
- requirement: &27203120 !ruby/object:Gem::Requirement
28
- none: false
29
+ requirement: !ruby/object:Gem::Requirement
29
30
  requirements:
30
- - - ! '>='
31
+ - - ">="
31
32
  - !ruby/object:Gem::Version
32
- version: 0.9.0
33
+ version: '0'
33
34
  type: :runtime
34
35
  prerelease: false
35
- version_requirements: *27203120
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - ">="
39
+ - !ruby/object:Gem::Version
40
+ version: '0'
36
41
  - !ruby/object:Gem::Dependency
37
42
  name: rspec
38
- requirement: &27202300 !ruby/object:Gem::Requirement
39
- none: false
43
+ requirement: !ruby/object:Gem::Requirement
40
44
  requirements:
41
- - - ~>
45
+ - - ">="
42
46
  - !ruby/object:Gem::Version
43
- version: 2.3.0
47
+ version: '0'
44
48
  type: :development
45
49
  prerelease: false
46
- version_requirements: *27202300
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
52
+ - - ">="
53
+ - !ruby/object:Gem::Version
54
+ version: '0'
47
55
  - !ruby/object:Gem::Dependency
48
56
  name: bundler
49
- requirement: &27201380 !ruby/object:Gem::Requirement
50
- none: false
57
+ requirement: !ruby/object:Gem::Requirement
51
58
  requirements:
52
- - - ~>
59
+ - - ">="
53
60
  - !ruby/object:Gem::Version
54
- version: 1.0.0
61
+ version: '0'
55
62
  type: :development
56
63
  prerelease: false
57
- version_requirements: *27201380
64
+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
66
+ - - ">="
67
+ - !ruby/object:Gem::Version
68
+ version: '0'
58
69
  - !ruby/object:Gem::Dependency
59
70
  name: jeweler
60
- requirement: &27200760 !ruby/object:Gem::Requirement
61
- none: false
71
+ requirement: !ruby/object:Gem::Requirement
62
72
  requirements:
63
- - - ~>
73
+ - - ">="
64
74
  - !ruby/object:Gem::Version
65
- version: 1.5.2
75
+ version: '0'
66
76
  type: :development
67
77
  prerelease: false
68
- version_requirements: *27200760
69
- - !ruby/object:Gem::Dependency
70
- name: rcov
71
- requirement: &27199840 !ruby/object:Gem::Requirement
72
- none: false
78
+ version_requirements: !ruby/object:Gem::Requirement
73
79
  requirements:
74
- - - ! '>='
80
+ - - ">="
75
81
  - !ruby/object:Gem::Version
76
82
  version: '0'
77
- type: :development
78
- prerelease: false
79
- version_requirements: *27199840
80
83
  description: Fasta reader, ORF emitter, sequence translation
81
84
  email: pjotr.public01@thebird.nl
82
85
  executables:
@@ -89,7 +92,7 @@ extra_rdoc_files:
89
92
  - LICENSE.txt
90
93
  - README.md
91
94
  files:
92
- - .travis.yml
95
+ - ".travis.yml"
93
96
  - Gemfile
94
97
  - Gemfile.lock
95
98
  - LICENSE.txt
@@ -133,37 +136,26 @@ files:
133
136
  homepage: http://github.com/pjotrp/bigbio
134
137
  licenses:
135
138
  - MIT
139
+ metadata: {}
136
140
  post_install_message:
137
141
  rdoc_options: []
138
142
  require_paths:
139
143
  - lib
140
144
  required_ruby_version: !ruby/object:Gem::Requirement
141
- none: false
142
145
  requirements:
143
- - - ! '>='
146
+ - - ">="
144
147
  - !ruby/object:Gem::Version
145
148
  version: '0'
146
- segments:
147
- - 0
148
- hash: 2941883289909211187
149
149
  required_rubygems_version: !ruby/object:Gem::Requirement
150
- none: false
151
150
  requirements:
152
- - - ! '>='
151
+ - - ">="
153
152
  - !ruby/object:Gem::Version
154
153
  version: '0'
155
154
  requirements: []
156
155
  rubyforge_project:
157
- rubygems_version: 1.8.10
156
+ rubygems_version: 2.0.3
158
157
  signing_key:
159
158
  specification_version: 3
160
159
  summary: Low memory sequence emitters
161
- test_files:
162
- - spec/emitter_spec.rb
163
- - spec/predictorf_spec.rb
164
- - test/doctest/test_fasta.rb
165
- - test/doctest/test_frames.rb
166
- - test/doctest/test_getorf.rb
167
- - test/doctest/test_paired.rb
168
- - test/performance/translate_with_biolib.rb
169
- - test/performance/translate_with_bioruby.rb
160
+ test_files: []
161
+ has_rdoc: